The Queensland and Federal governments are butting heads over cyclone recovery funding.

Queensland Deputy Premier Jackie Trad has slammed a Federal Government decision to pay just $29.3 million of the $110 million the state wanted for its proposed $220 million Cyclone Debbie recovery program.

But the Prime Minister says most of the money Queensland wants is for projects that are not technically ‘disaster relief’, and accused the state of trying to use the assistance package as a slush fund.

“[The disaster funding scheme] is not designed to fund new infrastructure. It is designed to fund recovery and repairs and reinstatement and so forth,” Mr Turnbull told reporters.

“The request from Queensland was carefully assessed in accordance with the rules and funding has been applied in accordance with the rules.”

The state was seeking $60 million for a flood levee in Rockhampton to prevent a repeat of this year's floods, and proposed a $40 million upgrade for the Whitsunday Coast airport.

Ms Trad said previous federal governments funded similar mitigation infrastructure as ‘disaster relief’, including upgrades to Brisbane's ferry terminals in the wake of the 2011 floods.

“If that application had been put in now, it would have been rejected. This is the kind of mean-hearted federal government that we have under Malcolm Turnbull,” she said.

Ms Trad said the state would have to rethink its plans.

“Our money is there, it's in the budget, that won't change ... so we're going to have to go back and re-look at this,” she said.

“We're going to have to talk to the communities and the mayors of these councils and have a conversation about where we go to from here.”