The reopening of the centre on Christmas island, which was closed in 2018, has been announced a few months before an election in Australia.
"My job now is to ensure the boats don't come", Morrison said.
Tuesday's development was a major blow to Prime Minister Scott Morrison's minority government's highly controversial immigration policy.
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.
"My job now is to ensure that the boats don't come... to..."
PM Scott Morrison approved reopening Christmas Island after a legislative defeat in Parliament allowed refugees and asylum seekers detained in existing offshore centres to travel to Australia for medical treatment.
The fast-tracked medical transfers law will only apply to refugees and asylum seekers already on Manus Island and Nauru.
Under the previous system, the Minister for Home Affairs, now Peter Dutton, had final say over all proposed medical transfers.
The Prime Minister during question time this afternoon dug the boot into Labor over national security concerns emerging from the bill.
"Have no doubt this man sitting opposite me is not fit to be the prime minister of this country", Mr Dutton said of the Opposition Leader.
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Opposition Leader Bill Shorten chose not to turn the government's defeat into a call for an early election, arguing the new law was a humanitarian change that made no significant adjustment to offshore processing of boat arrivals.
In Geneva, Philip Lynch, director of the International Service for Human Rights (ISHR), welcomed the new law and said that Australia's system has "deliberately dehumanised" refugees and asylum seekers for decades.
"This legislation is confined to the current cohort of people on Manus Island and Nauru", said Kerryn Phelps, an independent lawmaker.
John Coyne, a former Australian Federal Police officer now at the Australian Strategic Policy Institute, said the law was well-constructed but it did "change the narrative", which could encourage some people to risk a boat journey.
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.
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.
But criticism of the camps has grown amid reports of abuse, suicides and lengthy detention periods, even as the government says the policy is discouraging asylum seekers from embarking on unsafe sea voyages.
Opinion polls consistently show the Labor Party easily taking control of the government in the election.
He pointed out the medivac bill only applied to asylum seekers and refugees now stranded on Manus Island and Nauru.