The State Government has dumped plans to use commercial fishermen to bait and destroy large sharks at popular metropolitan beaches, opting to use its Fisheries Department instead.

The government originally planned to use commercial fishermen to manage baited drum lines off Perth and South West beaches, catching and killing sharks over three metres in length.

But the Fisheries Minister, Ken Baston, says threats from opponents have prompted a private fishing outfit to pull out of the process.

"We had a successful tenderer, but that tenderer did pull out with the worry of threats to himself and his family," he said.

Mr Baston said other fishing outfits had applied for the tender but had been knocked back.

"I'm told that the panel reviewed all those tenderers," he said.

"The others weren't successful, for the reasons I'm not sure."

Mr Baston says while a commercial fishing outfit will still manage South West beaches, the metropolitan area will be patrolled by officers from the Department of Fisheries.

"I met with Fisheries officers this morning, and they're happy, they gave me the information that they did have a boat available, and what they need," he said.

He said he hoped the use of fisheries officers was a short-term measure, and that a professional fishing outfit would eventually take over.

Questions over use of fisheries officers

The Opposition's Dave Kelly says the government needed to come up with a different plan.

"I think the government should take a cold shower on this issue, it's far too important for them to continue to cobble together a policy," he said.

"They should take a deep breath, they should not go ahead as planned, they should go back to the drawing board, they should come up with a policy that will actually work."

Mr Kelly also questioned why fisheries staff were being used to implement the policy when private outfits had refused.

"The Premier can't simply say 'well if the commercial fishers won't tough it out, we'll just order our own staff to do it'," he said.

"The Premier has to tell the community what the concerns were, and how they will be addressed for Fisheries' own staff."

Mr Baston insisted fisheries staff would be protected but would not be drawn on the specifics.

"We need to discuss that, and obviously I won't disclose how we do that now," he said.

"Because we've got people who are prepared to put out those threats that they have."

Mr Baston also said the Commonwealth had this morning given the tick of approval for the policy, which was originally prohibited by federal law.

"Under the Act, we have to have approval to take out protected species, i.e. the white pointer," he said.

"That has been approved."

In a statement, the federal Environment Minister Greg Hunt said the government believed the increased risk of shark attacks in WA was a matter of national significance.

He said the government had decided it was in the national interest to temporarily exempt the WA government from the relevant provisions of its Environment Protection and Biodiversity Conservation Act.

Mr Baston would not say exactly when drum lines would be set in the metropolitan area, but said it was likely to be in the coming weeks.

Catch and kill policy referred to EPA

Meanwhile, the WA Conservation Council has referred the Government's shark catch and kill policy to the state's environmental watchdog for assessment.

Council director Piers Verstegen said he was yet to hear back from the Environmental Protection Authority but did not believe it could avoid assessing the plan.

"Taking sharks out of the marine system has a major impact on the ecology of those systems but there's also other species that are going to be seriously impacted," he said.

"Under the Western Australian Environmental Protection Act, there's a responsibility for the EPA to assess any proposals that would have a major impact on the environment.

"Now this proposal is going to deliberately have a major impact on endangered sharks but it's also going to have a major impact on other threatened species in the ocean; dolphins, sea turtles, whales.

"These things need to be investigated, previous investigations have shown that this proposal is going to have a serious impact on those species and that needs to be done now in relation to the Barnett Government's cull proposal.

"It really is something that's going to have a very significant impact on our marine environment."

In a statement, the EPA said it was yet to consider all the information in the referral.

It said it would be seeking advice from relevant agencies before making a decision on whether or not to assess and, if so, what level of assessment should apply.