Waitemata District Commander Superintendent Bill Searle confirmed he was aware of the allegations. But he refused to comment on what injuries the prisoner sustained, whether the officers stood down were still being paid and whether criminal charges were likely.
"These allegations are currently being investigated. The officers have been stood down from duty while the investigation process is being carried out," he said in an emailed statement.
The Independent Police Complaints Authority is also investigating.
A police source said the officers that came forward showed integrity. "It was really quite a big thing to do."
Traditionally, officers are stood down when serious assault allegations are made.
In 2004 South Auckland Senior Sergeant Anthony Solomona was stood down while police investigated claims he assaulted five male complainants.
Christchurch Sergeant Kerry Joyce was stood down for about 16 months in 2004 after allegations over an arrest in Cathedral Square.
A builder claimed in court that Joyce kicked him in the mouth while he was on the ground, causing him to lose teeth. Joyce was charged with assault with intent to injure but found not guilty at trial.
In 2003 South Auckland police officer Alexander Grant was sentenced to 16 months in prison after he assaulted a handcuffed man in the back of patrol car.
The Manukau District Court heard Grant punched and elbowed the man up to 20 times, at one stage knocking him unconscious.
In 2001 a Whangarei police officer quit after allegations he broke into a police cellblock and assaulted a prisoner.