One guard, aged 34, has been charged with causing grievous bodily harm with reckless disregard, and a second, 26, has been charged with assault with intent to injure.
A third man, aged 31, has been charged with attempting to pervert the course of justice.
Auckland Prison director Andy Langley said Corrections is working closely with police following the incident.
"Immediately following the incident, I reported it to Police and made changes to the management of the wing where the incident took place.
"It also came to my attention that standard procedures in the event of use of force were allegedly not followed - this too was referred to Police," he said.
Three staff were suspended after the incident, Langley said.
A Corrections inspectorate report into the incident, and any connected incidents, is under way alongside a full operational review, he said.
A scheduled inspection of Auckland Prison is also being carried out by the Corrections Inspectorate, under a new inspection regime introduced this year. Prisoner welfare will be looked at as part of the in depth review.
"Corrections has a zero tolerance to violence policy. No assault or violent behaviour by a prisoner, or a staff member, is acceptable," Langley said. "Anyone who takes part in this kind of behaviour can expect to be prosecuted."
Neither Police nor Corrections would comment further as the matter is before the courts.