Air passengers can now refuse to go through a security scanner on health grounds or privacy reasons, just as the government introduces such scanners at 11 further airports.
But passengers refusing to go through a scanner will have to submit to a private search by security staff.
Previously, those refusing to go through scanners were not allowed to fly, as private searches took time and could potentially slow security queues.
Security scanners are currently in operation at 10 of the UK's largest airports. They were deployed in response to the threat to aviation posed by non-metallic improvised explosive devices.
Transport secretary Patrick McLoughlin said he was now deploying security scanners at Stansted, Luton, Bristol, Liverpool, Newcastle, Aberdeen, Leeds Bradford, East Midlands, Prestwick, Cardiff and Belfast City airports.
He said: "In the UK, all security scanners now use millimetre wave technology, which has no known health risks, and which is quite different from x-ray technology.
"Furthermore, all security scanners deployed now use automatic threat recognition software, which means that no image of a passenger is produced, thus alleviating any residual health or privacy concerns."
But, he added: "I appreciate a small minority may still prefer to request an alternative procedure for a variety of reasons.
"From today, passengers who opt out of being screened by a security scanner will be allowed a private search alternative. This is a method of screening which we consider is of an equivalent security value to a security scan.
"These revised arrangements will be kept under review to ensure that high levels of security are maintained whilst avoiding disproportionate impacts on airports and passengers."
Those refusing a private search, which involves loosening or potentially taking off some clothing, will not be allowed to fly.