It took just two minutes for surging seas off the NSW Central Coast to rip more than 80 shipping containers from the deck of a stricken Taiwanese cargo ship, the first report into the incident reveals.

The YM Efficiency, a 43,000-tonne Liberian-registered ship, was travelling from Taiwan to Sydney when it was hit by huge seas off the coast of Port Stephens sending 81 containers tumbling into the ocean and a further 62 containers damaged.

The Australian Transport Safety Bureau today said it was at about 12.30am on June 1 when the ship was hit with a "period of quick, heavy rolling for about 60 to 90 seconds".

It took just two terror filled minutes for cargo ship to lose 80 containers off NSW coast. Picture:9NEWS (9news)

The ship's master estimated the 268-metre vessel was twisting 30 degrees port and starboard in the seas as the alarms went off.

The main engine was shut down and loud noises were heard on the deck.

Efficiency's second officer turned on the deck lights and saw containers had been lost and damaged.

Two minutes later the rolling had subsided and the master took control of the drifting ship.

A report from the Australian Transport Safety Bureau says the ship "hit a period of quick heavy rolling for about 60-90 seconds." Picture: 9NEWS (9news)

The ATSB's preliminary report found the crew had checked the container lashings multiple times before the storm and had logged the deteriorating weather.

Authorities worked feverishly to locate and map the drifting containers which posed severe risks to other boats in the water.

For weeks after the incident, locals and Roads and Maritime Services removed tonnes of debris during clean-up efforts as plastic began washing up on pristine beaches as the cargo burst from damaged containers and floated ashore.

A hydraulic survey vessel was also brought in by the Australian Maritime Safety Authority, as arranged by the shipping company's insurer, to search the ocean floor as the clean-up continued into mid-June.

A final report into the incident which littered Port Stephens beaches with debris isn't expected until mid-2019. Picture: 9NEWS (9news)

The clean up cost tens of thousands per day. Picture: 9NEWS (9news)

The shipping company, Yang Ming, apologised to locals and promised to pay for the clean-up, estimated at tens of thousands of dollars per day.

The investigation is still underway and the ATSB will examine the Efficiency's container stow and lashings, its stability, the actions of officers and crews and weather conditions during the incident.

The final report is not expected until mid-2019.