Experts feared the 'naked' body scanners, which use X-ray technology to show up hidden explosives or weapons, could emit harmful levels of cancer-causing radiation.
Critics also said the machines invaded passengers' privacy and the radiation they generate raised the risk of cancer. Some Muslim groups also refused to walk through them on religious grounds.
The move in Europe begs the question -- why are they still allowed in the United States? Hundreds of the devices are in use at least 68 airports across the nation.
New trials of the device, which display a 'naked' image of the person being scanned, were blocked by the European Commission last November.
But Manchester Airport, the only airport in Europe using the USD 130,000 machines, was told it could continue using them for another year.
Now, after the machines have come to the end of their three-year trial, European Commission chiefs have failed to give their approval for their full time use, the Daily Mail reported.
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EC bosses eventually declared the risk was 'close to zero' in a report in May --and Manchester airport expected the technology would be approved for permanent use.
But bosses were left waiting for the green light and now said they have been left with no option but to axe the 16 security machines because Brussels legislation does not allow security trials to exceed a three-year period.
Manchester airport introduced the scanners as part of a security pilot in October 2009, but will now have to scrap the machines by the end of next month.
The scanners have been controversial among flyers since they were introduced in force at US airports in 2010.
The Transportation Security Administration (TSA) began installing hundreds of the devices after the foiled Christmas Day, 2009, attempt to blow up a Detroit-bound passenger jet with an underwear bomb.
The TSA insists that research shows the devices do no emit harmful levels of radiation, but the issues is far from settled in the minds of many flyers -- some of whom opt for full-body pat-downs instead of passing through the machines.
In a red-tape wrangle, USD 1.8 million will be splashed out on new 'privacy-friendly' machines at Manchester and the recruitment of an extra 55 full-time security officers, who will manually frisk passengers.
The new scanners will use radio-frequency technology instead of X-ray radiation.