Fisheries and Aquaculture Minister Phil Heatley endorsed the principles of the industry's "Managing Our Own Ship" strategy at the final day of the Seafood Industry Council's (SeaFIC) annual conference.

The industry has called for reform to give it more autonomy over its activities. It has claimed the government and Fisheries Ministry should focus on setting clear standards on quotas and environmental restrictions, leaving implementation to the industry, leading to big cost savings and improved productivity.

"I applaud that view, I want you to know that I endorse it and I'm supportive of it," Heatley said.

While the government would continue to keep tight control of environmental standards such as quotas and the impact on seabirds, it was pragmatic about how the industry operated so long as it was within those standards, he said.

"We're interested in outcomes, what you do out on the water on your boats is your business, it is the outcomes that we're focused on." Heatley said he saw clear opportunities for efficiency gains.

The industry has said the savings could run into billions of dollars. "The government spends millions of dollars in research into the deep sea fishery, but so does the industry, so it seems absurd that we would be funding two sets of administration systems, two sets of quality control systems."

Cath Wallace, a senior lecturer at Victoria University, said there had been no consultation on the plan although the minister was aware that other fisheries stakeholders were unhappy about it. "The ships might be theirs, but the environment and the fish are not."

Wallace said that it was inappropriate for the fishing industry, which has very strong vested interests, and have shown that they do not look after the resource, to be put in control of it.

While it was easy to measure emissions on a factory, Wallace said it was much more difficult to apportion blame for damage to an ecosystem. "There's absolutely no knowing who is responsible, you know it is the fishing industry as a whole, but there is no knowing which companies should be held accountable."