There is a dark side to archaeology that is seldom acknowledged in Indiana Jones films; namely a long tradition of using excavations to prop up nationalist and colonial claims; to confirm (or occasionally challenge) the truth of religious and classical texts; and to present an idealised picture of groups seen as "ancestors".

Things get particularly fraught in relation to the Middle East and "biblical archaeology", yet the same fundamental issues - ethical, political and methodological - apply all the way from Maiden Castle to Machu Picchu.

In the Balkans, argues Evangelos Kyriakidis, lecturer in archaeology at the University of Kent, "archaeology has been very significant for national identity". It "played an important role in 19th-century international sympathy towards the Greek national cause; today, the Kosovo issue has important archaeological extensions. Both Greece and the former Yugoslav republic of Macedonia use archaeology in their arguments against each other."

But can archaeologists working outside war zones remain immune to ideological influences, conscious or unconscious, which direct them towards what to look for and then convince them that they have found it?

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Even if individuals inevitably have their biases and blind spots, can the discipline as a whole incorporate the kind of self-correcting mechanisms we find in the other sciences? Can it offer us any kind of objective truth, however partial and tentative, about the past - or will it always be tainted by politics?

In 1985, Richard Wilk, now professor of anthropology and gender studies at Indiana University, published a paper, The Ancient Maya and the Political Present, which clearly hit a raw nerve. "It was widely derided at the time," he says. "Some Mayan archaeologists still won't talk to me."

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Wilk's argument was simple: there is no written evidence for classic Maya culture or its "collapse", so any theories have to be based on archaeology. Many different ones have been put forward. Yet all of them, Wilk argued (and even illustrated with a graph), reflected current concerns: "almost every trend of importance in recent United States history finds some reflection ... in learned analyses of the rise and fall of ancient Maya civilisation".

The Vietnam War, the vogue for hallucinogenic drugs, environmentalism, the women's movement, and anxieties about population growth or "big government" all subliminally affected how scholars accounted for the end of the Maya, Wilk said.

Wilk claimed that our images of the past were influenced by the present - and that this was a good thing. "If the past bore no relation to the present," he argued, "it would be dreadfully boring, even to archaeologists."

The stories we want to hear about prehistory are those that either legitimise present courses of action or offer warnings about what we should not do. Although Wilk denied that he was taking the extreme position that "archaeologists are just making up stories about the past", he was certainly undermining any straightforward claims that they could offer us direct access to prehistory.

This view is supported by Adam Stout, research fellow in archaeology at the University of Wales, Lampeter, and author of Creating Prehistory: Druids, Ley Hunters and Archaeologists in Pre-war Britain (2008). He worries about the naive view that "better science, better technology, better recording, better techniques will give us an ever more accurate understanding of the past". Although "archaeology today is a broad and on the whole very tolerant church," he says, he fears that "the beasts are gathering".

"Archaeology is being driven towards the disciplinary stockade, with the results-driven, answers-not-questions ethos so apparent in TV archaeology, in developer-driven archaeology and increasingly within academic archaeology as archaeologists struggle with research assessment exercise delivery schedules and the need to be seen as productive."

So do archaeological methods reveal any sort of truth about the past? Stout is cautious. "The past is a devious, amorphous entity," he says, "very resistant to being skewered by posterity. Nothing about it stays still for long, from the tiniest detail to the grandest of grand narratives; it gets constantly rewritten and re-interpreted. I do think that archaeology is essentially a hall of mirrors - but none the less valid for that. Mirrors are interesting things."

Some argue that archaeology is becoming more genuinely scientific and objective. Margarita Diaz-Andreu, leader of the history of archaeology research group at Durham University, makes a distinction between the questions archaeologists ask, which are "very much influenced by our own experiences as people", and the rigour of their methods. "There are more and more techniques/scientific approaches in archaeology to answer our questions," she says.

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Others dispute this. Ethan Cochrane, lecturer in archaeology at University College London, argues that "there is no archaeological science (yet). (We) use other sciences to explain various aspects of artefacts, asking questions such as: where did the raw materials for this artefact come from? How old is this piece of pottery? What is the isotopic signature of this bone? But the science behind these investigations is not archaeology - it is chemistry, physics and biology. Archaeologists take the answers and use them as data to weave stories about the past."

But what happens when outsiders start to "weave stories" about other groups of people? Cochrane is a specialist in the Pacific Islands and notes that in Fiji, where the local people have political power and own most of the land, "their position is not threatened by anything my research might say".

In Hawaii, by contrast, "the native population is a colonised and oppressed group", while archaeology "is practised largely by whites and in the context of commercial/rescue archaeology in a scientific vein ... Many see archaeology as yet another act of colonisation and an affront to Hawaiian culture - white people telling Hawaiians what their history means. Archaeology in Hawaii is highly political, as one might imagine, when international corporations owned by non-Hawaiians build luxury hotels and in the process disturb Hawaiian burial grounds."

A more striking example is provided by Egypt, argues Lynn Meskell, professor of anthropology at Stanford University. The tourist trade demands Nile cruises, luxury hotels and beautifully presented archaeological sites. Many Egyptians, meanwhile, are expected to provide local colour by living in picturesque poverty or performing a pantomime version of Ancient Egypt in a reconstructed pharaonic village. This has made tourism a source of resentment and even violence - and archaeology can hardly claim neutrality.

As this may suggest, there are ethical as well as methodological reasons why archaeology is now much more systematic and self-conscious about examining its own assumptions - and whose interests they serve. Meskell addresses this in Cosmopolitan Archaeologies, a book she is editing for Duke University Press that is due to be published later this year.

For Clare Fawcett, assistant professor on the anthropology programme at St Francis Xavier University in Nova Scotia, the values that have damaged archaeology in the past can and should be replaced by others.

"Archaeological work has been used to justify extreme nationalist ideologies such as those of Nazi Germany and Imperial Japan in the 1930s and 1940s," she says, "but it can also reflect more benign notions of group identity, including nationhood. Today, archaeology in former colonies such as Canada often tells the story of indigenous peoples' histories. This deepens understandings of 'nationality' for all citizens.

"Rather than trying to make archaeology a 'pure' and 'untainted' science, I think the best way to ensure that it is not used to support problematic political movements is for archaeologists to constantly question the assumptions embedded in archaeological interpretation. They can do this by asking whether these interpretations can be supported by the evidence and if there are other interpretations. Archaeology cannot answer the question of what to believe, it can only limit the kinds of stories people tell about history and the past."

This is an impressive ideal, but Fawcett admits to a difficulty that brings us right back to the controversies surrounding "biblical archaeology"; namely that "one person's 'problematic political movement' is another's valued belief system."

SEEK AND YE SHALL FIND: THE POLITICISATION OF BIBLICAL ARCHAEOLOGY

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Few areas of academic dispute can be as acrimonious as "biblical archaeology". And since it is located at the intersection between two viciously contentious issues - the conflict between science and religion, and rival claims to Israel/Palestine - this is hardly surprising.

Paul L. Maier, Russell H. Seibert professor of ancient history at Western Michigan University, has proclaimed that: "The spade remains the Bible's best friend."

Many places mentioned in Scripture, including Abraham's home town of Ur, have been excavated to reveal buildings of the biblical era. The fallen walls and layers of ash discovered at Jericho can be plausibly dated to the time of Joshua. Archaeological finds of the early 20th century confirmed the existence of a major Hittite empire hitherto unknown outside the Old Testament.

An obelisk depicts King Jehu kneeling before the Assyrian ruler, Shalmaneser III. The name of King David is independently attested on a victory stele found in 1993. And so it goes on. Critics ignoring such evidence are dismissed by one of Maier's allies as peddling "postmodern malarkey".

Others claim that biblical archaeology is often sustained by an overtly Christian agenda. One of the founding fathers of the discipline, William Foxwell Albright (1891-1971), was clearly influenced by his background as the son of evangelical missionaries. Convinced of the historical truth of much of Scripture, he has been criticised for seeing the role of archaeologists as "to illuminate, to understand and, in their greatest excesses, to 'prove' the Bible".

Such reservations are developed further by researchers such as Nur Masalha, reader in religion and politics at St Mary's University College, Twickenham. In The Bible and Zionism: Invented Traditions, Archaeology and Post-Colonialism in Israel-Palestine (2007), Masalha argues that biblical archaeology "was established to validate Western roots in the Holy Land and authenticate the historicity of the Hebrew Bible. Virtually all biblical archaeologists were Western Christians or Jews with a strong commitment to the historicity of the Bible, and interpreted their findings in the light of the Scriptures."

Seek and ye shall find. One of the core questions about archaeology, biblical and otherwise, is how much people find what they are looking for, which is often itself influenced by religious, political and ideological factors. In the 1870s, in archaeology's early, romantic days, Heinrich Schliemann's excavations at Troy, Mycenae and Ithaca were clearly intended to confirm the historical truth of ³ÉÈËVRÊÓƵr's Iliad and Odyssey.

Finds were presented - not to say marketed - as King Priam's treasury or the mask of Agamemnon. Furthermore, since he identified the level known as Troy II with the ³ÉÈËVRÊÓƵric city, Schliemann hacked through the layers above it (which may well have a better claim) to gain access. Focusing on and resurrecting one stratum of the past can often mean neglecting or destroying others.

When it comes to the issue of archaeological "proof" for the Bible, much of the acrimony focuses on Philip Davies, Niels Lemche, Thomas Thompson and Keith Whitelam, a group known variously to their critics as "minimalists", "the Gang of Four" and the "Copenhagen school" (although Davies and Whitelam are now based in Sheffield).

Despite many differences, they tend to give a late date for the composition of the Bible and, crucially, play down the amount of genuine history it contains. In assessing the results of excavations, they say they always believe in asking, "If we did not have the Bible, how would we interpret the archaeological evidence?"

This seemingly innocuous question opens up a whole can of worms. Would the building unearthed at Magiddo ever have been interpreted as a stables if we hadn't read that King Solomon kept his horses there? Can we find traces of King David's capital city or his golden goblets? Is there any hard evidence on the ground for the Exodus, the conquest of Canaan - or even for a distinctive group we can identify as the Israelites?

Even where the facts are not disputed, this still leaves plenty of room for scholarly dispute. If we find independent confirmation of the existence of 12 biblical kings, does that count as a little or a lot? How far is absence of evidence just a matter of chance, which a new discovery may change tomorrow, and how far can it be used to argue that a particular event did not happen? (How much would we know about the Norman Conquest if we did not have written records?)

It would be hardly surprising if scholars slugged these issues out in learned journals and occasionally got abusive. But the temperature of the debate is positively vicious. Thompson claims that he and his colleagues have been called "a danger to Western civilisation", guilty of "intellectual dishonesty on the scale of Holocaust denial". And some of them give as good as they get.

The cause of this rancour is easily pinpointed. Whitelam's book, The Invention of Ancient Israel (1996), is subtitled "The silencing of Palestinian history". Davies writes that "Biblical scholarship inevitably focuses on the Israelite identity of a land that has actually been non-Jewish in terms of its indigenous population for most of recorded history ... Our focus on a short period of history a long time ago participates in a kind of retrospective colonising of the past. It tends to regard modern Palestinians as trespassers or 'resident aliens' in someone else's territory".

Masalha draws a similar moral. Traditional biblical archaeology, he says, was "Eurocentric and deeply ideological" - and "central to the Palestine conflict". Yet the latest research, he says, shows that "Canaanites and Israelites never existed as opposing peoples fighting over ancient Palestine. Perhaps this teaches us an important lesson: to resist the construction of 'separation barriers' or imaginary racial and ethnic divides between Israelis and Palestinians."

There is little doubt that archaeology did play an important role in Israeli nation-building. The passionate interest in archaeology by public figures such as the military leaders and politicians Moshe Dayan and Yigael Yadin, and the significance given to the "last stand" at the fortress of Masada, helped forge tighter emotional bonds between people and land.

But although Israelis, like fundamentalist Christians, are in some sense interested parties in the archaeology of the Holy Land, that hardly discredits their efforts per se.

For Sean Kingsley, visiting fellow at the Research Centre for Late Antique and Byzantine Studies at the University of Reading (and managing editor of the archaeological magazine Minerva), "the politicisation of archaeology in Israel is championed by the right-wing minority. Secular Israel is actually very mature in its approach to its heritage, digging up Islamic ships as very rare and scientifically crucial and carefully excavating and publishing Ummayad and Abbasid remains." There are also some Israelis in the "minimalist" camp.

The current British Museum exhibition Babylon: Myth and Reality (until 15 March) touches on many related themes. It brings together some of the magnificent reliefs from Nebuchadnezzar's palace with artworks inspired by the stories of the Hanging Gardens, the Tower of Babel, Belshazzar's Feast and Daniel in the lions' den.

It also features some of the cuneiform tablets that (although curator Irving Finkel admits they look about as interesting as dog biscuits) provide the social history to bring the biblical narratives down to earth. And highly relevant to all this, of course, were Saddam Hussein's absurdly grandiose plans to turn Babylon into a monument to his own glory. Like Jerusalem, the city remains very much a contested site. Few can hope that peace in Middle Eastern archaeology is going to break out any day soon.

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