Labs at University College London and the universities of Cambridge, Oxford and Glasgow have been affected by what has been described as a "real crisis" for certain types of brain research.
A major supplier of the gas to labs in the UK said a global lull in natural gas production, of which helium is a by-product, was causing demand to outstrip supply.
The shortage mainly affects magnetoencephalography (MEG) scanners, which are similar to magnetic resonance imaging (MRI) scanners but use super-cooled helium that needs to be topped up regularly.
Ray Dolan, a professor at UCL's Wellcome Trust Centre for Neuroimaging, said that the college had stopped taking bookings for its scanner after its supplier, BOC, said it could not guarantee how much helium it could provide. "It is rendering programmes that are funded very, very problematic and there's great uncertainty," he said.
Richard Henson, a programme leader for the Medical Research Council Cognition and Brain Sciences Unit, said that the scanner at Cambridge had been shut since Christmas.
"Nearly all MEG sites in the UK and the world" were affected, he said, and at least two projects at Cambridge were on hold.
Sven Braeutigam, head of physics at the Oxford Centre for Human Brain Activity, said the university expected its MEG scanner to shut down in late January.
"We keep optimistic and reckon that a downtime of four to six weeks would be bearable, but anything longer could have quite devastating consequences," he said.
At Glasgow, scans were scaled back before Christmas to save helium.
Professor Dolan said that UCL had contacted other suppliers, but they had not been able to guarantee that they would have any surplus helium to sell and would charge double the price of BOC.
"It could become extremely expensive," he said.
He added that in the long run it might be possible to synthesise helium at much greater cost, but "in the short term there is a real crisis".
MEG scanners, which cost ?1 million to ?1.5 million, detect magnetic signals within the brain rather than the blood flows tracked by MRI scanners as a proxy, Professor Dolan explained.
"If you want to really measure how regions of the brain interact during cognition, it's much more optimal [than MRI] because it's closer to the physiology [of the brain]," he said.
Nick Ward, business manager for special products at BOC, said that the global economic slowdown had created a "lull" for gas producers in areas including Algeria and Qatar that was reducing helium production as a side-effect.
For some time, artificially cheap stores of helium from the US had been filling the needs of users at low prices. However, Mr Ward said, the US supply has now hit peak capacity and that buffer from the vagaries of the market was coming to an end.