The numbers were temporarily halved after new strains of coronavirus emerged in the UK and South Africa.
NSW will return to a cap of about 3000 people a week from February 15, while Queensland is reverting to 1000. Victoria will increase its weekly hotel quarantine capacity to 1310 and SA has agreed to take 530 people a week. WA will retain its halved cap of 500 until the end of the month.
Prime Minister Scott Morrison announced the increased caps after a national cabinet meeting with state and territory leaders on Friday.
The federal government is also investigating doubling capacity of the Howard Springs quarantine facility in the NT from its current level of 850.
Queensland's proposal to use Toowoomba's Wellcamp Airport for two-week stays in isolation is also under consideration.
Mr Morrison said both would be for extra capacity rather than replacing capital city hotels.
Queensland and WA pushed for quarantine to be shifted out of hotels after coronavirus scares triggered snap lockdowns in Brisbane and Perth. Victoria also raised new isolation facilities after a hotel worker contracted the disease. But the prime minister signalled there would be no imminent changes to the quarantine regime.
"Hotel quarantine is the primary, and remains the primary system for running quarantine in this country. It has been incredibly effective," Mr Morrison said.
Chief Medical Officer Paul Kelly said there would always be a risk of human error but noted the small number of quarantine breaches.
"There is absolutely a need to continually improve the quality of our quarantine. It is already really top-class," he said.
Department of Prime Minister and Cabinet secretary Phil Gaetjens and the top public servants from each state and territory have been tasked with analysing Australia's risk environment.
That work will look at future pandemic management with the prime minister hopeful it could lead to more uniform responses across the states on issues like border closures.
Mr Morrison said other options for quarantine could emerge over the year as risks change.
"Australia, I suspect, will be ahead of the world in our risk environment, as we already are right now. That may enable us to do some things that they can't do in other places," he said.