The X-ray machines have been brought in at Manchester, Gatwick and Heathrow.
But scientists say radiation from the scanners has been underestimated and could be particularly risky for children.
They say that the low level beam does deliver a small dose of radiation to the body but because the beam concentrates on the skin - one of the most radiation-sensitive organs of the human body - that dose may be up to 20 times higher than first estimated.
Dr David Brenner, head of Columbia University's centre for radiological research, said although the danger posed to the individual passenger is 'very low', he is urging researchers to carry out more tests on the device to look at the way it affects specific groups who could be more sensitive to radiation.
He says children and passengers with gene mutations - around one in 20 of the population - are more at risk as they are less able to repair X-ray damage to their DNA.
Dr Brenner, who is originally from Liverpool but now works at the New York university, said: 'The individual risks associated with X-ray backscatter scanners are probably extremely small.
'If all 800 million people who use airports every year were screened with X-rays then the very small individual risk multiplied by the large number of screened people might imply a potential public health or societal risk. The population risk has the potential to be significant.'
Following trials, the airport scanners were officially introduced at Manchester Airport in January, at Heathrow Terminal 4 in February and at Gatwick in May this year.
The most likely risk from the airport scanners is a common type of skin cancer called basal cell carcinoma, according to the academic.
The cancer is usually curable and often occurs in the head and neck of people aged between 50 and 70. He points out it would be difficult to hide a weapon on the head or neck so proposes missing out that part of the body from the scanning process.
'If there are increases in cancers as a result of irradiation of children, they would most likely appear some decades in the future. It would be prudent not to scan the head and neck,' he added.
He recently aired his concerns to the Congressional Biomedical Caucus in the US - members of Congress who meet to exchange ideas on medical research.
Dr Brenner urged them to look at his concerns but said it was important to balance any health issues against passengers' safety when flying.
He said: 'There really is no other technology around where we're planning to X-ray such an enormous number of individuals. It's really unprecedented in the radiation world.'
The Civil Aviation Authority, Department for Transport and Health Protection Agency insist that the technology is safe and say their tests show it would take 5,000 trips through the scanner to equal the dose of a single chest X-ray.
They said in the climate of high security, it is essential that security staff use 'all means possible' to minimise risks to airline security.
The CAA said: 'The device has been approved for use within the UK by the Department for Transport and has been subjected to risk assessments from the Health Protection Agency.
'To put the issue in perspective, the radiation received from the scanning process is the equivalent to two minutes radiation received on a Transatlantic flight.
'Recent press publications have been a little alarmist and may have heightened concern in frequent travellers who may worry about their repeated exposure.
'Under current regulations, up to 5,000 scans per person per year can be conducted safely.'
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