The Maritime Union of Australia has agreed to end its industrial action at Patrick Terminals at its wharves in Sydney, Melbourne, Brisbane and Fremantle.
The announcement of the breakthrough came on Thursday after a marathon two-day conciliation hearing before the Fair Work Commission which Patrick Terminals hailed as a victory. However, the union said the waterfront dispute had been deferred not resolved.
Patrick CEO Michael Jovicic said he was pleased the union had "called off the damaging actions around Australia".
The union had inflicted unnecessary pain across the supply chain and had now walked away with nothing, Mr Jovicic said in a statement.
"Having lost in the court of public opinion they decided to retreat to fight another day," he said in a statement.
MUA National Secretary Paddy Crumlin said he was dismayed the company had rejected a reasonable and fair peace deal from the union that would have brought the dispute to an immediate end.
Nevertheless, the union had agreed to end all industrial action ahead of a two day hearing scheduled in the FWC for October 26.
The dispute escalated this week with Prime Minister Scott Morrison accusing the union of extortion, and Patricks saying essential goods like medication were stuck on the wharves while dozens of cargo ships were stranded off the coast unable to dock.
The union disputed the claims, saying it was used to "baseless attacks by the government".
In a revised offer to the company on Thursday, the union wanted to extend the rollover period of the existing workplace agreement to two years along with the industry standard of 2.5 per cent a year pay rises.
Mr Crumlin said the deal collapsed after the company insisted workers choose between substantially lower pay rises, or changes to the existing agreement that would allow the massive casualisation of the workforce.
"Resolving this dispute requires compromise from both sides. The union did that with our offer of a genuine peace deal, yet Patrick is instead forcing workers to choose between sacrificing their job security or losing money," he said.
Mr Jovicic said during negotiations on Thursday the MUA had rejected a 1.5 per cent pay increase each year for four years with no changes to their current conditions or rosters.
Patrick says it offered to hire 50 new workers at Port Botany to help clear the backlog of containers and improve productivity, as well as job guarantees with no forced redundancies for the life of the agreement.
Mr Jovicic said he was amazed the MUA had rejected the offer.
"At least now we can get on with clearing the backlog which exceeds more than 100,000 containers around Australia. My operations team estimate it will take between two and three months to return to normal."
"Hopefully this means we will avoid shortages of goods at Christmas time."
Patrick said a container with essential diabetes medication would be urgently discharged from Port Botany on Thursday night.