Fewer than 10 children remain on Nauru and that number will continue to drop before the end of the year, Prime Minister Scott Morrison says.
A push to urgently transfer sick asylum seekers on Manus Island and Nauru to Australia has been put off until next year.
But Mr Morrison denies it was to save the federal government from a humiliating parliamentary defeat - the first of its kind since 1929.
"Labor and a lot of people down here (in Canberra) were saying that," the prime minister told the Nine Network on Friday.
"The government confidently maintained its position in the House of Representatives, as we did for the last three months."
Mr Morrison said there would be "about six" children left on Nauru in coming weeks and people have been removed from detention when medical issues arose.
"All the children that have had medical-related issues for transfers have been transferred," he said.
"In some places, people are transferred to Taiwan or Port Moresby for medical treatment and they receive it."
The legislation would allow critically ill refugees to be flown to Australia for medical treatment on the advice of two doctors.
Mr Morrison accused Labor and the Greens of playing political games instead of actually caring about the refugees and that the laws would undermine border protection.
Labor Leader Bill Shorten said politicians needed to take the advice of medical professionals.
"I'm not going to start pretending as a politician that I'm a better doctor than the treating doctors," he told reporters on Friday.
Manager of Opposition Business Tony Burke said the bill did nothing to compromise national security and Mr Morrison was playing political games.
"We're not afraid of making sure that people in Australia's care are in a situation where the government has to listen to medical advice," he told ABC Radio on Friday.
Independent Sydney MP Kerryn Phelps - who has been driving the new laws - is determined for them to be dealt with when parliament resumes next year.
"If we have to wait until February at least there is, I believe, a light at the end of the tunnel," Dr Phelps told Sky News on Thursday.
Dr Phelps said the coalition had been spreading misinformation about her bill.
Australia's border protection policies will not be affected by the changes, because a minister will still able to stop the temporary transfers on national security or character grounds, she said.