The Department of Fisheries and Oceans is denying any irregularities in a program to buy fishing boats and equipment for native fishermen.

Federal officials spent $160 million to equip Mi'kmaq fishermen following the Marshall decision from the Supreme Court of Canada in 1999.

But in 2001, auditors could not find a paper trail for how bureaucrats spent millions of dollars buying fishing boats, licences and fishing gear from non-native fishermen.

David Balfour, in charge of aboriginal policy and governance for DFO, said the department quickly improved its bookkeeping practices and no funds went astray.

"All the money has been accounted for. We can account for every penny."

Auditors also questioned arrangements where brokers would set prices for boats and gear, and then negotiate sales agreements with the department.

Balfour admits DFO was rushing to get Mi'kmaq fishermen on the water, particularly because of concerns after a violent protest in Burnt Church, N.B, but said every deal the department cut was fair.

"I don't think that we overpaid in any instance, and the subsequent audits demonstrated that we have achieved value for money in our acquisitions."

Balfour said the issues raised by the audit were quickly resolved within the DFO, which is why the report was never publicly released.

The audit came to light as a result of a two-year, access-to-information struggle between DFO and the Halifax Chronicle-Herald newspaper.