Michael Adebolajo, 28, reportedly lost two teeth as he was restrained during an incident at Belmarsh high security prison in southeast London on Wednesday.
Adebolajo, charged with the murder of Drummer Lee Rigby is said to have claimed he was "targeted" by prison officers.
"We can confirm that an allegation of assault was passed to the Metropolitan Police Service on 17 July by Belmarsh Prison. An investigation has been started," a Metropolitan Police spokesperson said.
Rigby was hacked to death in broad daylight before Adebolajo delivered an Islamist tirade to passers-by. British Prime Minister David Cameron joined thousands of mourners last week at the soldier's funeral. Cameron gathered with some 800 of Rigby's family members and colleagues for the private military funeral at a church in Bury, near Manchester in northwest England.
All five men deny that they have assaulted Adebolajo.
Meanwhile, Prison sources told 'The Times' that the incident occurred when several officers were trying to "control and restraint" the prisoner as he refused to obey their instructions.
It is understood that several officers were called to help to restrain Adebolajo when he began to act violently. Five officers have to be present every time he is unlocked and returned to his cell in the high security prison.
"Prison staff do not attack prisoners. We feel that the Ministry of Justice missed an opportunity to correct false reporting of events at Belmarsh," POA chairman Peter McParlin said.
Adebolajo's brother Jeremiah said that the accused called his family and told them he was bleeding and had lost some teeth.
The British Muslim convert of Nigerian descent is charged with murder and possessing a revolver. He is also accused of the attempted murder of two police officers. His alleged accomplice, Michael, is charged with murder and possession of a firearm.
