The guards then escorted aboard a replacement crew who immediately began sailing the carrier towards Singapore.

The ship had been docked in the far south-west Victorian port of Portland for two months, with its sacked Australian crew refusing to sail it to Singapore where is to be scrapped.

At 1am Wednesday, a contingent of security guards — estimated by the Maritime Union of Australia to number more than 30 — boarded the ship, woke the five crew members on board, handed them their passports and escorted them down the gangplank.

Shortly after a replacement crew, believed to be foreign seafarers, was escorted on board.

By dawn, Portland residents awoke to discover the ship that has hauled alumina from Western Australia to Portland's Alcoa aluminium smelter for the past 27 years was nowhere to be seen.

"This is the worst example of guerrilla tactics to get rid of Australian workers since Patricks," said the MUA national secretary, Paddy Crumlin.

In 1998, the Patrick Corporation locked workers out of their port operations, and dogs and balaclava-wearing security guards were used.

The 40 Australian crew members of the MV Portland have lost legal actions in the Fair Work Commission and the Federal Court, where they argued the Federal Government's "temporary coastal licence", which allows Alcoa to replace the MV Portland with a foreign-flagged vessel and foreign crew, was invalid.

The MUA claimed the ship could not be sailed to Singapore because of a shortage of seafarers available to operate it.

Opposition Leader Bill Shorten labelled the midnight raid "disturbing" and "Work Choices on water".

"I'm deeply disturbed that we're seeing Australian seafarers being marched off ships, replaced by foreign seafarers.

"If nothing else, a government in Australia should stand up for Australian jobs," Mr Shorten said.

"What we see here is Work Choices on water being introduced by the back door with a nod and a wink by Malcolm Turnbull and his Liberals," he said.

Mr Shorten said in addition to concerns about Australian jobs, he was also worried about national security and protection of the local environment.

"There's an industrial dispute but that's the tip of the iceberg. What we see is Australian seafarers, Australian jobs being replaced by foreign seafarers, foreign jobs on our coastline," he said.

​ACTU assistant secretary Scott Connolly described the early morning raid as "an attack on Australian workers and their families that has no place in a modern Australian workplace".

"An acceptance that people can be forcibly removed from their place of work in an orchestrated midnight action should send shivers down the spine of all Australian workers," he said.

Employment Minister Michaelia Cash said: "it is not for industrial parties to pick and choose which orders of the Commission they will comply with.

"If the obligation to follow orders of the independent umpire is only seen as optional, then the integrity of the entire Fair Work system is put at risk".

Alcoa has stated the replacement of the MV Portland and its Australian crew will save the company $6 million a year.

Alcoa said it took "decisive action today to end protracted illegal industrial action".

"Alcoa has been extremely tolerant and given the MUA and its members every opportunity to stop their illegal industrial action," the managing director of Alcoa Australia, Michael Parker, said in a statement issued on Wednesday morning.

"Instead, the MUA has held our ship hostage for two months; disrupting the lives of other crew members, disrupting operations at the Port of Portland, and threatening the Portland community with the loss of cruise ship visits."

In fact, the MV Portland crew moved their ship last week and anchored in the bay, allowing a cruise ship to berth.

Another cruise ship, the Pacific Eden, berthed in Portland on Wednesday morning at a berth that had not been occupied by the MV Portland.

"This was very meticulously planned," Mr Crumlin said.

"You don't just get a foreign crew in five minutes — Alcoa would have had to have been planning this over weeks, while saying they were willing to talk to work out a solution.

The Australian Maritime Safety Authority would have had to be complicit, too, to give clearance to this replacement crew before they sailed.

"They've sacked an Australian crew just before Christmas and then used a cynical tactic of thuggery like this to get rid of them."