Australia's security agencies are in a "race against time" to do background checks on asylum seekers after medical evacuation laws cleared parliament.
Attorney-General Christian Porter said up to 300 people on Manus Island and Nauru could secure immediate medical approval to come to Australia.
But Labor says the coalition has already brought 900 people to Australia from the two islands under the previous laws and none have gone back.
Mr Porter fears that some detainees may have been accused or convicted - but not yet sentenced - in relation to serious crimes.
"We have been racing against time to find the people that will be subject to these transfers," Mr Porter told parliament on Thursday.
"Home Affairs now faces the task of assessing 1000 people in a timeframe essentially determined by a very small group of doctors.
"We reasonably believe that we will be forced with a flood of about 300 immediate 'Labor transfer' cases."
The legislative changes, which passed against the wishes of the Morrison government, allow immigration ministers to refuse medical transfers to convicted criminals.
But the coalition is worried this discretion hinges on the length of prison sentences.
The laws will only apply to people currently offshore and will not apply to any future boat arrivals.
But Prime Minister Scott Morrison said the changes have weakened Australia's borders.
"The only thing the Labor Party will turn back is they will turn back the successful border protection polices that this government has put in place," he said.
"They are weak and their weakness will infect this nation."
Opposition Leader Bill Shorten accused the coalition of rolling out the welcome mat for people smugglers by suggesting Australia's borders are now less secure.
"I totally repudiate the attacks of the government, seeking to whip up fear and hysteria, seeking to lure people smugglers to entice people onto boats to come to Australia," he told reporters.
"They should be ashamed of themselves for luring people to Australia by somehow implying that this government hasn't got strong borders."
The Christmas Island detention centre will be reopened as part of the government's $1.4 billion response to the new laws.
Refugee advocate Ian Rintoul said many people on Nauru and Manus had been "denied medical treatment for months and even years".
The government, however, says asylum seekers on Manus and Nauru have adequate health care, with 60 medical staff employed on rotation on the islands.