The "no security scan, no fly" policy at British airports is to remain in place despite EU demands that passengers be allowed a pat-down search instead, ministers have said.

The transport secretary, Justine Greening, said the refusal to allow passengers to opt-out from scanning was justified by the security threat to Britain and would be imposed through powers under the Aviation Security Act.

"Those passengers selected for scanning will therefore not be able to fly if they are not willing to be scanned," Greening said.

She also said that the use of certain x-ray security scanners at some British airports will not be banned despite European commission concerns about the health risks.

Ministers are to wait for further scientific work before deciding whether to ban the use of so-called "backscatter" scanners.

Brussels has halted all new trials of the machines while a safety report is compiled because of concerns that they could cause long-term health damage including cancer. In the UK, the Health Protection Agency has said they are safe for travellers to go through as many as 5,000 times a year and deliver a radiation dose equal to that received naturally in two minutes of flying at high altitude.

Greening held out the prospect that privacy concerns raised by the introduction of full body scanners, which reveal an outline of the body shape, would be addressed by software in development.

She said the software would mean that images would no longer be seen by human reviewers and airports will be expected to deploy it when they renew or replace equipment.

New security scanners, including the full body and x-ray "backscatter" scanners, have been in use at Heathrow, Gatwick and Manchester airports since February 2010 following the 2009 Christmas Day airline bomb plot.

A Department of Transport consultation on the use of the scanners has generated more than 6,000 responses. Many people said they were uncomfortable with having their body image captured for analysis and would prefer a pat-down search. American airline passengers on internal flights are offered this alternative if they have concerns about the scanners.

In a written ministerial statement, Greening said the government was only aware of 12 people refusing to go through the scanners at British airports out of more than one million scans since their introduction.

Greening said she had rejected the option of a pat-down search on security, operational and privacy grounds, adding: "I do not believe that a pat down search is equivalent in security terms to a security scan.

"The purpose of introducing security scanners in the first place was to protect the travelling public better against sophisticated terrorist threats. These threats still exist, and the required level of security is not achieved by permitting passengers to choose a less effective alternative."

She said a full pat-down search in a private room, that would involve the loosening or removal of some clothing, would involve an even greater intrusion of privacy and was an alternative for which very few passengers would opt.

It would mean far more disruption at airports, as staff would need to be diverted from the main search area to do the job. "I do not believe that this represents a viable way forward," she said.

Greening said the government had the right to reject the European parliament's proposal to give passenger a right to opt out of the scans.