Authorities say shipping containers that toppled from cargo ship YM Efficiency off the NSW coast may never be found, as investigators assess whether the ship's owner could have prevented the disaster.

The Liberian-flagged ship lost 83 containers in rough conditions off Port Stephens on Friday, with officials saying just one container has been retrieved as most could be at the bottom of the ocean.

An Australian Maritime Safety Authority (ASMA) told SBS News that authorities were looking to determine whether the YM Efficiency’s crew had been following international conventions when the containers fell into the sea. 

She said the investigation will focus on how the cargo was stored and secured, as required by the Safety of Life at Sea Convention. The outcome of the investigation will be made known in the next few days.

The stricken Taiwanese vessel docked at Port Botany on Wednesday morning where it was met by AMSA and Australian Transport Safety Bureau officers.

The container ship YM Efficiency arrives at Port Botany in Sydney, Wednesday, June 6, 2018.

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‘Complicated Jenga’

The 43,000-tonne ship berthed at 9.25am on Wednesday and authorities say it could take up to a week to unload the remaining containers.

Sydney Harbour Master Philip Holliday said it will be tricky unloading the 30 damaged containers from the ship.

"It is a complicated game of Jenga," Mr Holliday told ABC radio.

Aerial footage of the stern of the vessel showed a section of containers lying at an angle, along with several badly crushed containers.

Debris continues to wash up on beaches, with officials saying the clean up could last for months.

A map of the clean up area.

NSW RMS

Search for containers

Representatives for Yang Ming, the company that owns the ship, apologised to the NSW coastal communities affected by the debris wash-up.

"We will take full responsibility to recover and to minimise the impact to the marine environment,” Steven Ka said.

The company's insurers have hired a private company to help recover the containers.  

Roads and Maritime Services (RMS) NSW are in charge of the cleanup and the search for missing containers.

AMSA is assisting in the search, flagging locations where sunken containers may be and where they are likely to float ashore.

A container from the YM Efficiency washed up on Yacaaba Headland at the entrance to Port Stephens, Wednesday, June 6, 2018.

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RMS Director Angus Mitchell said only one of the lost containers had been recovered. Two were also spotted on Saturday but have not been seen since, according to reports.

Mr Mitchell said heavy rains hitting the NSW coast this week have hindered the search.

"Given the conditions and particularly the rain that we've had over the last few days, we haven't been able to locate any," Mr Mitchell said.

"Whilst we believe the vast majority are very likely at the bottom of the ocean, we won't know that for sure for some time yet."

Clean up begins

On Wednesday, the RMS deployed a 12-metre harbour cleaning vessel into the water off Port Stephens to help clean up the debris.

So far it has netted more than 30 skip bins full of container materials. The shipping containers that toppled into the sea were carrying mostly furniture, car parts and cosmetics. The greatest danger to the environment is from soft plastics.  

Up to 100 contractors using specialist machinery have joined the clean up along the coast.

“Three of our environmental services officers have also been relocated from Sydney to operate the vessel  - joining in the waterside contingent of boats and divers – to remove debris from the water using skimmers and other equipment,” Mr Mitchell said.

“The shoreline clean up is continuing with the 100 strong team of workers doing such a good job that there are considerably reduced quantities of material now visible along the coastline between Seal Rocks and Anna Bay.”

He said it was fortunate there had been no reports of injured wildlife or vessel strikes since the containers toppled into the sea. He noted that whale and dolphin migration season had started.

YM Efficiency, while making its way from Taiwan to Sydney last week was hit by heavy swells about 30km off the coast of Port Stephens.

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Who will pay for it? 

Mr Mitchell said the next stages of clean up are hard to predict and will be dependent on weather and ocean conditions.

“The possibility of the sunken containers breaking up could change the situation.”

He reiterated all costs associated with the clean up will be passed on to the ship owner’s insurers.

So far debris has been confirmed at Jimmys Beach, Rocky Point, Fingal Head, Bennetts Beach, Port Stephens from D’Albora Marina to the north of Little Beach, and Yacaaba Headland. 

While he understood the public was eager to help, he discouraged this for safety reasons, saying that debris in the ocean was subject to Australian Customs and Quarantine regulations.

“We want to reassure the community that we have no intention of scaling down this clean up effort until we are satisfied that our waters and coastline are back to their pristine condition," he said.

To report debris, call 13 12 36.

- Additional reporting by AAP.