An initiative to flag potential terrorist threats at an Boston airport has led to to widespread racial profiling of passengers, it was reported Sunday.

A report by the New York Times found that more than 30 federal officers involved in the "behaviour detection" programme at Logan International Airport said that the operation targets black and Hispanic people as well as those of a Middle Eastern appearance.

The claims will come as an embarrassment to air security chiefs, who had been touting the initiative as a model for transport hubs across the US. It also comes at time when the Obama administration has attacked the use of racial profiling by law enforcement authorities in Arizona and elsewhere.

The programme was brought in to allow officers to stop, search and question passengers deemed to be acting suspiciously.

Under the initiative, specially trained "assessors" would monitor security lines at check-ins and pull aside those observed to be displaying tell-tale signs – such as avoiding eye contact, fidgeting or sweating.

Passengers considered suspicious are then taken away for more intensive questioning.

But the system has led to de facto racial profiling, it is claimed. Thirty-two officers have submitted written complaints to the Transportation Security Administration (TSA) over the targeting of minorities by colleagues.

Some of the stop and searches were the result of pressure from manager who hoped that it would lead to the discovery of drugs, outstanding arrest warrants and fraudulent immigration documents.

As a result, assessors have been looking for people who fit certain profiles – such as Hispanics travelling to Miami, or black people wearing baseball caps backwards, it is claimed.

"They just pull aside anyone who they don't like the way they look – if they are black and have expensive clothes or jewellery, or if they are Hispanic," one white officer told the New York Times.

In an anonymous complaint to the TSA obtained by the newspaper, an officer wrote: "The behaviour detection program is no longer a behaviour-based program, but it is a racial profiling program."

Passengers have also complained of the seemingly discriminatory practice.

Kenneth Boatner, a black psychologist and educational consultant, was detained for nearly half an hour while attempting to travel to Atlanta on business last month. Agents examined belongings – including patients' clinical notes – after singling him out.

In an interview with the New York Times, Boatner said he felt humiliated and that the officers never explained why he had been targeted.

But he suspected it was because of his race and attire – he was wearing sweat pants, a white T-shirt and high-top sneakers at the time.

"I had never been subjected to anything like that," Boatner said.

In a statement, the TSA said the programme at Logan "in no way encourages or tolerates profiling" and that passengers are not allowed to be pulled aside based on their nationality, race, ethnicity or religion.

"If any of these claims prove accurate, we will take immediate and decisive action to ensure there are consequences to such activity," the agency added.