The Federal Government is gearing up for an election fight on border protection after its historic defeat on the floor of Parliament over medical care for asylum seekers.

Key points: The bill will be voted on in the Senate today, after the Government's historic loss in the Lower House

The bill will be voted on in the Senate today, after the Government's historic loss in the Lower House Scott Morrison and Peter Dutton are already warning of weakening of the nation's border protection regime

Scott Morrison and Peter Dutton are already warning of weakening of the nation's border protection regime Mr Dutton said he would implement the law, even though he did not support it

The Coalition is preparing to beef up border protection measures in response, foreshadowing announcements to be made in coming days.

For the first time since 1941, the Government lost a vote on its own legislation after Labor teamed up with the crossbench to pass amendments on the asylum seeker policy.

After the vote, the Government swiftly met with the Australian Border Force to put in place what Home Affairs Minister Peter Dutton called "contingency measures".

"The priority for me having met with the general of Operation Sovereign Borders is to deal with the difficult circumstance that Bill Shorten created," Mr Dutton told 7.30.

"I think most Australians now see fortunately before the election, unlike the case with Mr Rudd, a Labor Party unravelling a successful border protection policy.

"That's a disaster for our country."

Once the changes pass the Senate, asylum seekers could be transferred to Australia for medical treatment if two doctors agree they need it.

Adam Bandt, Andrew Wilkie, Kerryn Phelps and Julia Banks as the bill passed the House. ( ABC News: Andy Kennedy )

The decision can ultimately still be rejected by the Home Affairs Minister on security concerns.

Border Force officials briefed Mr Dutton and Immigration Minister David Coleman late last night.

Contingency plans discussed included the possibility of re-opening the detention centre on Christmas Island.

There are currently around 1,000 men still on Manus Island and Nauru.

Mr Morrison warned the changes would open the door to people smugglers, accusing Mr Shorten of weakening a policy that had stopped the boats.

"Every arrival is on Bill Shorten and Labor's head. Every arrival," Mr Morrison said.

"Every risk is on his head."

Sorry, this video has expired PM says Labor are soft on borders after losing key vote in House

But Labor's Manager of Opposition Business Tony Burke said there was no incentive for asylum seekers or people smugglers, as the new arrangements would only apply to those already on Manus Island or Nauru.

"Not one person who gets on a boat now will have their circumstances changed by what's happened in the Parliament. Not one," Mr Burke said.

Labor frontbencher Anthony Albanese said the party's position was simply about "doing the right thing".

"[Labor and the crossbench] were all prepared to sit down and get an outcome based upon the objective of looking after people in need," Mr Albanese said.

"That was it. Not about politics. Not about positioning."

The bill is not likely to have any issues passing the Senate, given the Greens and Labor have shown support for the measures.

Greens MP Adam Bandt has indicated the crossbench will also push to get other legislation the Government does not agree with passed by Parliament.

"There's now the chance we can take some action on climate change as well before the election is called," he told AM.