"It doesn't reflect what the fishery is like now," he said.
"We believe the work we did then and the work we did as a consequence has resulted in sustained behavioural change."
The fishing companies did not face any sanctions following the compliance audit.
"Prosecutions will have a short-term effect in terms of behavioural change," Orr said.
"We've modelled this in the past and, at best, it is three, four, maybe five years if you're lucky through prosecution action.
"What we achieve through risk profiling is signalling to the industry that we are paying particular attention, that we are analysing the data in great detail, and that we expect to see behavioural changes."
Prosecution was only used when rules had been breached by whole fleets of vessels owned by a single company, rather than a single vessel, Orr said.
DeepWater Group chief executive George Clement, whose organisation advocates for the industry, said the report was never disclosed to companies and it was difficult to respond immediately.
But he said remedial actions were put in place before the 2012 hoki season as a result of the ministry's analysis.
"This risk assessment was undertaken nearly a decade ago. Things have moved on a long way since then and the matters raised by MPI in this report have long since been addressed."
Fisheries Minister Stuart Nash said it was "totally unacceptable" behaviour by the companies.
He said he could not guarantee that dumping and discarding of fish was still occurring, but he was confident that practices had changed since the 2011 report.
"I don't want to make any excuses for past behaviour because it was unacceptable not only to me as the minister but also to the vast majority of New Zealanders and those in the fishing industry."
"We are going to make sure this is well and truly a thing of the past."
Nash said he was also considering the release of all reports on fisheries from the past 10 years.
Most of the hoki caught in New Zealand waters is exported to the US and Europe, and is famously used in McDonald's Filet'O'Fish burger. Exports are worth about $200 million a year.