BRISBANE'S City Cats and SES rescue vessels could be operating illegally from July because Queensland does not want to let the Commonwealth collect boat registration fees.

Transport Minister Scott Emerson yesterday confirmed he was awaiting more details from Canberra before he supported national domestic commercial vessel safety reforms, agreed to by the previous Labor Government.

His concern centres on the likely increased cost to commercial vessel owners, with registration fees set to jump as much as 300 per cent.

"The Queensland Government currently sets its commercial vessel and licensing fees at about 35 per cent of costs, but some states recover almost all costs," said Mr Emerson.

"This means the Gillard Government may triple the cost of Queensland commercial vessel licenses.

"That is unacceptable, which is why we will wait to see more detail before supporting the reforms."

However a Transport and Main Roads' departmental brief obtained by The Courier-Mail warned the national laws would take precedence over any state laws from July 1.

"The new national law will apply in Queensland regardless of whether the Queensland Government participates or not," said the brief dated April 19, 2013.

As a result, those vessels due to have their registration renewed in July would be operating illegally if the renewals could not be processed.

"This would also impact on the insurance coverage held by vessel owners as insurance is only valid if the operation is compliant with the necessary laws," advised the brief.

The document pointed out another 800 vessels would be up for registration renewal in August including 55 Coastguard vessels and about 40 volunteer marine rescue boats.

A spokesman for Minister Emerson said it was likely the Australian Maritime Safety Authority would appoint a separate agency to collect the fees to get around the problem, nothing had been finalised.

Changing to the national system will cost the State Government $2.5 million in foregone registration fees, and $550,000 in information and communication technology updates.

A spokeswoman for Federal Transport Minister Anthony Albanese said they were unaware of the Queensland Government's objection.

"On November 9, 2012, all states and territories agreed to sign up to the national maritime regulator," she said.

"All states and territories have committed to transitioning to the new arrangements."

Originally published as State fights federal boat licence rights