He said Mr Bain had "anguished'' over the prospect of returning to court and did so only reluctantly.
"The application is necessary because the minister has continued her policy of refusing to constructively communicate with his advisers, and because (Mr Bain) no longer has any confidence that his claim is being assessed in a fair manner.''
Ms Collins said the compensation application fell outside Cabinet guidelines and was entirely at Cabinet's discretion.
"I have taken steps to ensure the process is fair and proper throughout.
"Put simply, it would be unacceptable for Cabinet to base its decision for compensation on an unsafe and flawed report. That would not have resulted in justice for anyone, let alone Mr Bain.''
She said Mr Bain's request for the Government to put the compensation application on hold while a judicial review went ahead would only result in a further delay.
Ms Collins would not comment further while the matter was before the Courts.
The Ministry of Justice declined to to comment on the application, saying it was a ministerial matter.
Mr Bain's solicitor Michael Reed QC would also not comment while the case was before the courts.
Mr Bain was acquitted of killing five family members in 2009, and has made a bid for compensation for spending more than 13 years in prison for the murders.
A report by former Canadian Justice Ian Binnie found that on the balance of probabilities Mr Bain was innocent of murdering his parents, two sisters and brother in Dunedin in 1994 and had been wrongfully imprisoned.
Ms Collins had the report peer reviewed by former New Zealand High Court judge Robert Fisher, who found inaccuracies.
Last week, Prime Minister John Key said a further report into the compensation bid seemed likely.