Prime Minister Scott Morrison says he will restrict overseas arrivals, with a plan to go to the national cabinet on Friday.
NSW and Victoria had done the heavy lifting on quarantining international arrivals, and with international flights no longer landing in Melbourne, flights had been diverted to other cities, he said.
"I'll be taking a proposal to national cabinet to slow that down," he said.
Western Australia has called for lower arrivals in that state, but Mr Morrison said there was no strong case for Western Australia to take fewer. Each state should carry a share, he said.
"The issue is the overall level of returning Australians are and that's why I'll be bringing a proposal on Friday to reduce the load," he said.
"At this time we don't want to put any more pressure on the system than is absolutely necessary."
On March 20, the borders were closed to non-Australians Compulsory hotel quarantine began on March 28. From March 21 to June 30, more than 212,000 people had flown into Australia, the Border Force said. The number included air crew.
In the month from June 7, 39,394 people have arrived from overseas to NSW, 15,374 to Victoria, and 10,054 to Queensland. Lesser numbers have arrived in the other jurisdictions - 307 in the ACT, 962 in the Northern Territory, 683 in South Australia, and 5377 in Western Australia.
International flights into Melbourne have now been suspended. NSW Police said they had managed more than 34,400 people in hotel quarantine since March 29. On Wednesday, 5600 people were in quarantine in 22 hotels in Sydney.
But Mr Morrison said he Victorian lockdown had not changed his view that internal borders should remain open.
"Victoria has self isolated," he said. "My view about people moving from NSW to Queensland, or to South Australia or Western Australia has not changed...
"This is about Victoria isolating itself, not other states shutting themselves off to Victoria. There's a key difference in that."
He called on people who live in and around the NSW-Victorian border towns to stay put and not travel.
NSW Premier Gladys Berejiklian said the NSW government was considering compulsory 14-day quarantine for people returning to that state from Melbourne.