Morrison said the reopening of Christmas island centre would strengthen the capacity of Operation Sovereign Borders, the government's controversial border protection operation aimed at stopping boat arrivals to the country.
Mr Morrison pledged to reverse the laws if the coalition was re-elected at the upcoming federal election.
The bill passed in the House of Representatives by one vote after the Labor opposition, the Greens and crossbench MPs agreed on last-minute amendments.
The bill would become law without another vote if it is approved by the House on Tuesday.
"If we're sending people who really need [help] to Australia already, why make a big deal of it, and why create a symbol that says we're going to get even kinder?" "We can preserve our national security and still look after people to whom we owe a duty of care".
"I think most Australians now see fortunately before the election, unlike the case with (former ALP PM Kevin) Rudd, a Labor Party unravelling a successful border protection policy". The rules around medical evacuations only apply to existing refugees in offshore detention, not new arrivals, and the government still has the discretion to overturn the recommendation of doctors.
Also in the Swiss city on Wednesday night, Abdul Aziz Muhamat, a Sudanese refugee activist who has spent five years on Manus Island, won the Martin Ennals Award 2019, one of the most prestigious global human rights prizes, organizers said. The government had similarly made the offer only available to refugees on the islands at the time to avoid attracting new asylum seekers, Shorten said.
It is the first time in decades that an Australian government has lost a vote on a substantive piece of legislation, sparking applause and cheers from observers in the parliamentary viewing gallery in Canberra.
He was also told it could result in 1,000 asylum seekers transferred to Australia within weeks. The human rights body has urged the government to evacuate the remaining people still held on Manus Island and Nauru.
Christmas island, an Australian territory located on 380 km from Indonesia's Java island, was until 2012 the point of arrival of boats of undocumented migrants trying to seek asylum in the Oceanic country.
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