At least 30 skip bins worth of debris have already been cleaned off beaches since the containers toppled off the YM Efficiency when high swells unexpectedly hit the cargo ship off the NSW coast almost a week ago.

Divers, a garbage-collecting boat, sand comb, mini dozer and about 100 people have since been contracted to help pick rubbish off the sand, rocks and sea bed in and around Port Stephens.

NSW Roads and Maritime Services executive director Angus Mitchell said the ship owners will foot the bill for the clean-up.

"All of the costs will be passed onto the (ship's) insurance company and that is already starting to happen now," Mr Mitchell told reporters on Wednesday.

"It is very hard to speculate on how much this will cost but it could run into tens of thousands of dollars a day."

The Liberian-flagged ship sailed into Sydney's Port Botany where it docked outside the DP World terminal about 9.30am on Wednesday.

Botany Bay harbour master Philip Holliday said the ship's captain and about a dozen crew on board were "shaken" by the incident but uninjured.

"They want the whole thing sorted out so they can get back to their normal duties," Mr Holliday told AAP on Wednesday.

Mr Holliday estimated it could take about two weeks before the ship could set sail again, after noticing some damage to a gangway on its port side.

"There are (also) quite a number of boxes that are squashed and a couple are hanging over each side," Mr Holliday told AAP.

"It is quite a tricky operation for the terminal and the ship owners to lift the boxes off safely. I have been describing it as a complicated game of Jenga."

The Australian Maritime Safety Authority is inspecting the ship for compliance with requirements for cargo stowage, which is expected to be finalised in coming days.

The Australian Transport Safety Bureau has also launched an investigation to determine whether further action will be taken.

Australian Associated Press