The council's infrastructure committee was told 98 spots would be permanently lost as a result of Queen's Wharf, with a further 112 lost from mid-2017 to late 2018.

The losses constituted more than a third of the 600 inner-city motorcycle parking spaces the council introduced to the CBD between 2012 and 2015.

In response, the council has identified four priority sites for new motorcycle bays, which would add 94 new spaces at North Quay (37), Albert Street (10), Kurilpa Park at South Brisbane (24) and William Street, between Elizabeth Street and the Victoria Bridge (23).

The William Street site had already been delivered, Brisbane Infrastructure transport planning program director Lindsay Enright told the committee, with the rest due to be complete by the end of the month.

But that still left an immediate shortfall of 116 spaces.

A further five sites, at Gallipoli Place on Roma Street (79), Gardens Point Road (two locations with 30 spaces each), Alice Street (20) and the Queensland University of Technology's Gardens Point campus (TBC), had also been identified as future parking locations.

Infrastructure chairman Amanda Cooper said the council was working with the state government to replace the spaces, which would be done at the government's expense.

"Everybody's trying to get the right outcome," she said.

Liberal National Party administration councillor Kim Marx (Runcorn) said she was concerned ratepayers would be stuck with the bill for doing the state's work.

"They took what we put in at ratepayers' expense and it means that us, as local councillors, potentially miss out on park upgrades, new footpaths, all that sort of stuff," she said.

Cr Cooper, her LNP colleague, sought to allay those concerns.

"No, it doesn't, because we're actually negotiating with them so that we do the work on their behalf," she said.

"That's part of our discussion about them compensating us for work that we do on their behalf.

"... The fact is, the impacts of Queen's Wharf I don't think we're yet fully understood. We've had to make modifications and I think we'll continue to have to make some modifications to how this city works on an ongoing basis."

Labor opposition councillor Shayne Sutton questioned whether the council had negotiated costs with the state government, pointing to last year's dispute between the two levels of government over intersection upgrades necessitated by the Queen's Wharf development.

That $10 million dispute, Labor argued at the time, could easily have been avoided if the two parties had entered into a memorandum of understanding prior to the council conducting the work.

"I know there was a bit of a lack of clarity last year about the intersection upgrades that would need to be funded and who was paying for that and where that money was coming from," she said.

"At the time, I talked about the need to have some kind of up-front agreement like an MOU – are those kinds of discussions happening now in terms of the cost recovery?"

Cr Cooper said the council was working with the government on an "open book" process.

"They can see the expenditure that council is making and they are quite happy, I understand, with that process going forward," she said.