More than 4,000 cattle are being unloaded from a ship after it failed to safely sail from the port of Portland, in south-west Victoria, twice in a week.

MV Jawan timeline: November 22: MV Jawan attempted to leave the Port of Portland but was turned around by the pilot

November 22: MV Jawan attempted to leave the Port of Portland but was turned around by the pilot 780 cattle were off-loaded from the top of the ship in an attempt to fix the stability issues

780 cattle were off-loaded from the top of the ship in an attempt to fix the stability issues November 24: MV Jawan attempted to leave but was again turned back

November 24: MV Jawan attempted to leave but was again turned back November 26: Australian Maritime Safety Authority (AMSA) said the ship would not be released from detention with cattle on board

November 26: Australian Maritime Safety Authority (AMSA) said the ship would not be released from detention with cattle on board November 27: All cattle off-loaded from the detained ship

The Federal Department of Agriculture and Water Resources has launched an investigation into the circumstances surrounding the shipment of livestock on the vessel MV Jawan, operated by MarConsult Schiffahrt GmbH & Co KG, which was bound for Pakistan and Oman.

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The ship was prevented from leaving the port on both Thursday November 22 and Saturday November 24 due to "stability issues" and witnesses took video footage and photographs of the ship rocking from side to side.

In a statement to the ABC, an Australian Maritime Safety Authority (AMSA) spokesperson said: "[On Monday night] after discussions with the MV Jawan's operators and classification society, AMSA has determined that the ship will not be released from detention with cattle on-board given the stability issues had not been resolved.

"AMSA has informed the Department of Agriculture and Water Resources [DAWR] of our decision not to permit this shipment and understands that all cattle have begun to be removed from the vessel this morning after discussions between DAWR and the exporter.

"AMSA will not permit any further loading of livestock on this vessel until the cause of stability issues are confirmed. The vessel is free to depart without livestock onboard."

Unloading began Tuesday morning

Port of Portland chief executive officer Greg Tremewen said AMSA had advised his organisation late on Monday that the ship was not permitted to sail out of the port with the cattle on board.

"We simply got advised that the cattle had to be unloaded and the vessel's not cleared to sail until the cattle are removed," he said on Tuesday.

"Subsequent to that, the cattle will have to be unloaded from the vessel under the supervision of the Department of Agriculture … and that process has commenced this morning."

The ship MV Jawan had to unload more than 4,000 animals bound for the Middle East. ( Supplied: Allen McCauley )

Mr Tremewen said he estimated that the unloading process would take a day or two, and the animals were being put on trucks and transported from the port.

Previously an AMSA spokesperson said it had not detained the vessel after the first attempt due to concerns about the ship's seaworthiness because of the way it was moving.

The spokesperson said 380 of the 4,327 cattle on board were removed in an effort to improve the ship's stability, but when it sailed out again on Saturday there were still issues.

"AMSA is working with the vessel's classification society, technical experts and the vessel operators to determine how the issues can be resolved," they said.

The ship was forced to return to port after beginning to sway from side to side. ( Supplied: Allen McCauley )

Death of one animal unrelated to stability issues, department says

A DAWR spokesperson said the cattle started being unloaded on Tuesday morning after a decision from the exporter.

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The department previously said one animal had died, but the death was "unrelated to the stability issues experienced by the vessel".

A departmental vet is overseeing the unloading process and has reported no welfare or health issues among the animals, which are being returned to the feedlot.

"It remains the intention of the exporter to export the cattle at a later date," the spokesperson said.