The state and federal governments have spent months warring over where the new centre should go.

Premier Annastacia Palaszczuk has attacked the prime minister for rejecting her plan for a 1000-bed regional facility at Toowoomba, saying if he'd agreed it would already be open.

She's repeatedly warned that the use of hotels for quarantine increases the risk of coronavirus outbreaks because they are not set up for infection control.

"Our hotels were not meant to be the last line of defence for this type of infectious disease," she said this week in urging Scott Morrison to approve the Toowoomba plan.

In a letter late on Thursday, the prime minister again rejected Ms Palaszczuk's proposal, instead proposing a 1000-bed facility on Commonwealth land at the Damascus Barracks at Pinkenba, in suburban Brisbane.

Deputy Premier Steven Miles conceded on Friday that neither project would meet demand, and hotel quarantine will be needed regardless of the outcome.

"We would continue to envisage a level of hotel quarantine going forward under either proposal," he said. Currently there are about 3500 people in hotel quarantine in Queensland.

Mr Miles said Queensland was happy to proceed with a joint, formal assessment of the Pinkenba site, but said the state government had already considered it and rejected it, in part due to old, asbestos-riddled buildings on site.

He wants the prime minister to keep the Toowoomba proposal on the table, saying the plan is well advanced and therefore can be built more quickly, and is scalable beyond 1000 beds.

"I think what Queenslanders liked about the regional quarantine proposal was the distance between this facility and people's homes ... and an urban area," he said.

"This Pinkenba proposal is in the suburbs of Brisbane."

In his letter, Mr Morrison said Queensland's plan for a facility at Wellcamp Airport in Toowoomba did not meet his requirements including that it be on Commonwealth land, and within an hours' drive of a tertiary hospital.

Australian Associated Press