"The allegations were looked at at the time and there was no evidence of it," she told reporters.
The minister also dismissed the suggestion that the two reports indicated there was a long track record of organised violence at the Mt Eden prisons.
She argued that the two investigations were at different jails -- the old Mt Eden Prison, which closed in 2011, and the new MECF remand prison.
"It's not the same site, it's not the same prison, it's next door to it," she said. "Totally different organisation, totally different institution."
Serco took over the MECF in 2011, but Corrections stepped in and took over day-to-day control of the prison last year following reports of widespread violence and drug use among prisoners.
A draft report on violence within the prison was completed by the Chief Inspector of Prisons in September, but Serco is challenging it in the High Court.
The hearing in the High Court at Wellington is expected to wrap up today.
Labour Party corrections spokesman Kelvin Davis said the minister appeared to be making excuses.
"Old prison, new prison - same prisoners. Their behaviour is not going to change because the colour of the bars is different."
Mr Davis also said that if the 2009 investigation found no evidence of organised violence, "then it's gone to hell in a handcart by 2015 and it can all be attributed to Serco".