It is believed 42 Iraqi men were sent back to Baghdad in a forced return.
Thirty-six are reported to be still being held at Baghdad airport where they arrived early on Thursday.
The UKBA declined to comment on the specific allegations, but said minimum force would only be used as a last resort.
The deportation was carried out by the UK Border Agency in conditions of complete secrecy, with no information of any kind being given out.
The flight landed at around 0600 (0300GMT) at Baghdad airport on Thursday and journalists were not allowed any access.
Of the 42 deportees believed to be on board, only six were released swiftly.
One of them, Sherwan Abdullah, a Kurd, told the BBC he and others had been beaten by UKBA personnel to force him off the plane in Baghdad.
“They was grabbing us, they told us if you don’t come down, we’re gonna beat you badly, and we’re gonna take you out,” said Mr Abdullah.
Asked if this happened on the plane, he said: “Yes on the plane. If somebody wasn’t willing to come out, they grabbed them, they grab the neck, they nearly killed them, they nearly kill them, these people cannot breathe.”
Mr Abdullah also said that all his money have gone missing..
But 14 of the deported all told the UN refugee agency, the UNHCR, that they had been beaten by UKBA employees both to get them on the plane in London, and off it in Baghdad.
The UKBA said that a minimum amount of force would only ever be used as a last resort, when an individual became disruptive or refused to comply.