Industry superannuation fund Asset Super has questioned the federal government's decision to impose a levy on super funds to recoup the compensation provided to victims of fraud from the Trio Capital collapse.

"We calculated our levy under these new arrangements and it is about $330,000; that is $330,000 of members' money that needs to be paid into the pool of money for Trio Capital," Asset Super chief executive John Paul said.

"I don't see that as being particularly equitable that we as funds that do the right thing should prop up funds that do the wrong thing."

Paul said the cost of compliance had steadily increased over the years as the requirements had become stricter, and industry funds spent much time and effort in making sure they were compliant.

"That annoys me because we work as hard as possible to be compliant, and yet with all of that emphasis on doing the right thing, then you have some people who do the wrong thing and the government says: 'Well, we levy a fee across all of the good funds that are out there,'" he said.

He said he appreciated the political reality of compensating members of an Australian Prudential Regulation Authority-regulated fund, but hoped the government would do everything possible to recover the funds lost by Trio.

"I hope that's what they will do, rather than taking the easy way and put a levy on all the other funds and we will just let the others slide," he said.

Treasury last month announced it would charge 0.0001977 cents times the net assets of a super fund to recover the around $55 million in financial assistance, while the maximum levy is capped at $500,000.

The Association of Superannuation Funds of Australia (ASFA) said in a submission to Treasury that it supported the levy, but it did question the formula adopted by the department.

ASFA said especially the cap of $500,000 could result in a substantially worse outcome for members of smaller funds than members of large super funds.