A Yang Ming-owned container ship was arrested in Sydney on Sunday after the Taiwanese company failed to pay a $3 million bill for the recovery of containers lost off the Hunter coast.
The Federal Court Admiralty Marshall arrested the YM Eternity - the YM Efficiency's sister ship - about 6.50am in Port Botany.
The arrest came after the Australian Maritime Safety Authority petitioned the Federal Court to recover the outstanding debt.
The Newcastle Heraldreported on Saturday the bill had not been paid by the January 18 due date and AMSA was considering its options.
It is not the first time the YM Eternity has been subject to an arrest at the port.
The ship was detained by AMSA on July 12 last year for the same systemic failure to safely stow and secure cargo that led to the YM Efficiency container spill a year earlier.
AMSA said on Sunday Yang Ming was refusing to pay for the clean-up of the remaining pollution, including the containers and their contents located on the seafloor near Newcastle.
Sixty containers have been identified using remotely operated underwater vehicles. A further 16 are yet to be found and five were recovered shortly after the spill.
AMSA awarded Ardent Oceania a contract to recover the 60 identified containers in December. The contract is valued at about $15 million and work is expected to begin in March.
AMSA chief executive officer Mick Kinley said the YM Eternity arrest showed Australia would not allow international shipping companies to pollute its waters without consequence.
"If you pollute our waters and refuse to pay the price of cleaning up that pollution, we will hold you accountable," he said.
"Our ocean won't pay the price of Yang Ming's pollution - Yang Ming will."
The anticipated cost to locate and clean-up the 16 missing containers is up to a further $5 million, AMSA said, bringing Yang Ming's debt to $20 million.
Yang Ming's insurers have previously committed funds for underwater inspections and guidance technology for some commercial fishers.
Aus Ship, the Australian representatives of insurer Britannia P&I, said it could not comment on Sunday as the matter was before the courts.
The Newcastle Herald understands if the company or its insurer chooses to pay the outstanding amount, the ship will be released. If they choose to contest the payment, a proceeding will be held in the Federal Court.
The YM Eternity had been scheduled to depart Port Botany at 2pm on Monday for Melbourne.
The YM Efficiency remains in service and was in Shanghai on Sunday.