Queensland Treasurer Tim Nicholls says a disaster relief funding agreement between the State and Federal governments worked "pretty well" in 2011.

But he says he wants extra conditions this time.

Mr Nicholls says Queensland is dealing with massive recovery costs for the second time in two years.

"I would expect that the cost of rebuilding Queensland will be in the billions of dollars," he said.

He is negotiating a funding deal with the Federal Government.

There had been disagreement over the nature of the arrangements, but Mr Nicholls now says the National Partnership Agreement will be based on a 2011 deal.

"So there are some aspects that were good that we want to keep, there are some areas where some increased flexibility would assist," he said.

The State Government also wants to reintroduce a clause that would guarantee funding to repair council-owned infrastructure.

A draft agreement is expected to be ready by the end of the week.