However, it is not clear that this would trigger a constitutional crisis, and Mr Morrison told Sky News on Tuesday night he would not use the incident as a trigger for a snap election.
«If we lose that vote next week, so be it. We won’t be going off to the polls,» he said.
«The election is in May. I will simply ignore it and we’ll get on with the business.
«But I’m not going to be howled down by the Labor Party who want to dismantle a border protection system I had a key hand in building.»
The bill — brought by independent MP Kerryn Phelps, who replaced Malcolm Turnbull in the seat of Wentworth — would enable refugees on Manus Island and Nauru to come to Australia for medical treatment if that course of action is recommended by two doctors.
Currently, those decisions are controlled by the health systems on the two islands and the Department of Home Affairs, which has its own health team led by a chief medical officer.
Under the Phelps proposal, the Minister for Immigration would have a limited ability to block such a medical transfer on security grounds.
The government argues the bill, if successful, would undermine Operation Sovereign Borders.
«You just need two doctors on Skype who say ‘I can’t really see from here so you need to be brought to Australia so I can see you here’,» Mr Morrison argued on Tuesday night.
«Four hundred people will come — single males — from Manus Island [and] Nauru … which will overwhelm our detention centres.
«We’ll have to reopen Christmas Island. We’ll have to reopen detention centres that we were able to close because of our strong border protection policies.»
Mr Morrison also said there was no capacity under the legislation for a minister to reject a transfer for someone based on character grounds.
«Someone who’s a paedophile, who’s a rapist, who has committed murder — any of these other crimes — can just be moved on the say-so of a couple of doctors on Skype,» he said.
«This is a stupid bill. It’s written by people who haven’t got the faintest idea how this works.»
In a bid to head off defeat on the bill, Mr Morrison had offered to create an independent medical panel to oversee Department of Home Affairs decisions on medical transfers.
The panel would scrutinise decisions but would not have the ability to override them. Dr Phelps and other proponents of the proposed legislation dismissed that as unsatisfactory.
In 1929, when a government last lost a vote on legislation, then prime minister Stanley Bruce immediately called an election — which he lost. However, Dr Phelps has said she does not regard her bill as a vote of confidence in the minority Morrison government.
A question mark lingers over whether the bill has enough crossbench support to succeed, because independent MP Cathy McGowan has not committed her crucial vote either way.
In a blog post on Tuesday, constitutional law professor Anne Twomey suggested passing the bill could be slightly easier than first thought. She argued a standing order in the lower house that requires an absolute majority to overturn the agenda could in fact be unconstitutional.
That would mean a simple majority of 75 or fewer out of 149 (the Speaker does not vote except in a tie) could disrupt the order of business and bring on a vote on Dr Phelps’ bill.
Labor MPs indicated there was no mood in the party to abandon support for the Phelps bill, even in the face of a ferocious government campaign on border protection.
Asked about the issue at a press conference on Tuesday, Labor leader Bill Shorten affirmed his party would still vote for the bill. «That’s our position,» he said.
The matter is expected to come before the Parliament during its first sitting session of 2019 next week.
Michael Koziol is a political correspondent for The Sydney Morning Herald and The Age.