The APL England was en route to Melbourne from China when rough seas caused the shipping containers to topple overboard on Sunday.

The Australian Marine Safety Authority has laid charges against the master of the APL England for offences relating to pollution and damage of the marine environment as a result of poor cargo loading.

But operator ANL said the APL England's crew had done well to manoeuvre the ship to safety amid poor weather conditions.

The ship is now detained at the Port of Brisbane.

"This was an unnerving event, even for seasoned maritime professionals, and the captain and the crew have ANL's full support," the operator said in a statement on Saturday.

ANL also said it had contracted two companies to help with the clean-up, including the removal of debris and spilled containers.

Some 15 containers have been accounted for.

AMSA operations general manager Allan Schwartz handed down the charges against the ship master on Friday, a decision he said was not taken lightly.

"This and other incidents remind us of the important role the ship's Master has in ensuring the ships that ply our waters are operated safely and do not damage our marine environment," Mr Schwartz said in a statement.

The decision does not detract from the responsibility of the ship owner APL Singapore, insurer Steamship Mutual and ANL, he added.

ASMA also ordered $22 million from APL Singapore on Friday under the Protection of the Seas Act, which must be paid before the ship's release.

NSW Maritime acting executive director Alex Barrell on Friday said there were about 100 people working between Wollongong and Port Stephens to remove containers and their contents from beaches and bays.

Efforts were focused on Cronulla and nearby Sydney beaches at Little Bay, Maroubra and Tamarama, as well as at Newcastle and Port Stephens.

Australian Associated Press