The Opposition Australian Labor Party (ALP) joined forces with the Greens and independent Members of Parliament (MPs) to pass the medical evacuations bill by 75 votes to the governing Liberal-National Party coalition (LNP)'s 74.
The amended bill, which passed into law in the Senate shortly after Morrison's announcement, hands doctors on Nauru and Manus Island greater power to transfer asylum seekers to Australian medical facilities.
Morrison said he would repeal the "foolish law" if his government were re-elected. "Every arrival is on Bill Shorten [Leader of the Labor Party] and Labor's head".
It was the first time in decades that an Australian government has lost a vote on its own legislation in the House of Representatives.
Mr Porter said a refugee on Manus Island was facing sex abuse charges and someone on Nauru had been charged with indecently assaulting a child.
The Senate passed similar amendments on medical evacuations despite ruling party objections on the last day Parliament sat a year ago.
The Australian government said Wednesday it would reopen a mothballed island detention camp in anticipation of a new wave of asylum seekers arriving by boat after Parliament passed legislation that would give sick asylum seekers easier access to mainland hospitals.
Protesters marched along Sydney streets to demand all asylum seekers and refugees be brought to Australia, in Sydney, Australia, August 27, 2016.
"My job now is to do everything in my power, in the power of the government, to ensure what the Parliament has done to weaken our borders does not result in boats coming to Australia".
On Wednesday, Mr Morrison said the government would re-open the Christmas Island centre "to deal with the prospect of arrivals. and transfers" - arguing both were now more likely.
Labor leader Bill Shorten says his party is tough but fair on border control after it backed the bill.
The vote has paved the way for border protection to be a major issue in the general election, which Morrison on Tuesday said would be held in May despite the historic defeat.
The move cut short a furious debate over whether the vote in the lower house could be seen as a vote on a money bill and was therefore a vote of no confidence in the government itself.
"The legislation applies for people who are already there [on Manus and Nauru] - it does not apply to anyone new", he told reporters.
The changes included a provision that only the 1,000 asylum seekers now held on Nauru and Papua New Guinea and not any future arrivals would be considered for medical evacuation under the new regime.
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