"This is a pleasing outcome as it both recovers costs and gives more certainty over the future management of the prison," she said.
Corrections chief Ray Smith decided to return the Mt Eden prison into his department's control in response to high rates of violence and drug use among inmates.
Serco received several performance notices for these incidents, which meant it was unable to get its full performance-related bonus.
In December, Mr Smith confirmed that Serco's contract to run the prison would not be renewed at a break point in March 2017.
Ms Collins said Corrections would continue to manage the prison after Serco's contract ended, and a longer-term plan for the prison would be determined at a later date.
Serco signed a $300 million contract to manage the prison for 10 years in 2010.
The contract included a clause which allowed the contract to be reviewed, and potentially ended, after six years.
On top of the contract, the company was entitled to $1.2 million a year in performance-related fees.
In July, $565,000 was deducted from this performance-related payment because the company had failed to reduce serious assaults and provide safe custody to prisoners.
It was fined a further $300,000 during the 2014/15 financial year because of understaffing, mixing accused prisoners with convicted prisoners, and other offences.