The Australian Productivity Commission says regulators like the Australian Fisheries Management Authority should be allowed to make recommendations without interference from government.

In a recent report, the case of the Abel Tasman super-trawler was used to highlight the impact of political intervention in the regulatory decision making processes.

The Australian Fisheries Management Authority (AFMA) gave approval for the vessel to fish in Australian waters, but that approval was revoked by the federal Labor government of the day and a two year ban put in its place.

The Australian Productivity Commissioner Warren Mundy says governments should acknowledge that some risks cannot be eliminated.

"We weren't concerned with the decision per se, what we were concerned with was the fact that this business had gone through all the normal, known regulatory processes, and was ready and able to proceed, but for an intervention through the parliament," he said.

"That empowered the Minister for Environment effectively to stop the trawling activity after the organisation had done everything that was reasonably requested of them."

The reason for parliamentary intervention in this case was the high level of community concern raised in response to AFMA's approval.

"What our concern is, is not the matter of whether or not these fish should be taken, but rather that despite the fact that a independent government agency, operating with what it considered to be the best scientific evidence available had given consent effectively for the fisheries vessel to go and do its business," Mr Mundy said.

"The vessel was brought from overseas I understand, and basically the rules of the game were changed just as that vessel was about to deploy, in spite of the scientific evidence that it wasn't a big problem.

"Our concern is that the regulator had done its work, undertaken appropriate risk assessment, and then that risk assessment was essentially put to one side," he said.

The report, Regulator Engagement with Small Business, refers to comments made by AFMA regarding the impact of government intervention in decision making processes.

"Given current Ministerial actions, there is now no certainty in the legislation and management that in the past has been regarded as one of the best management systems in the world, and in fact suggests that the political process deployed to date may in fact have imploded the good work," the report says.

"This has reduced confidence in the independent body."

While the Commissioner stresses the fact that these instances are rare, he confirms they do serve to undermine certainty within the business community.

"Business need to have certainty and rely on regulatory frameworks," he said.

"There are circumstances where what appear to be robust, regulatory frameworks are put in place, they're proceeding, and then due to community pressure on politicians the parliament effectively moves the goal posts.

"That creates a particular degree of uncertainty," he said.

While the 400 page report references the Abel Tasman only briefly, it does make a recommendation.

"Governments should explicitly acknowledge that some risks cannot be eliminated, and that regulators should operate independently, and without undue interference from government in implementing risk management approaches," the report recommends.

"These acknowledgements should be incorporated in a public statement of governments' expectations of their regulators."