The captain and second officer of a ship that caused New Zealand's biggest sea pollution disaster pleaded guilty to criminal charges Wednesday and could face lengthy jail terms, officials said.

The officers were in charge of the Liberian-flagged Rena when it ploughed into a reef last year, releasing an oil slick that killed thousands of sea birds and fouled beaches in the North Island's pristine Bay of Plenty.

The men, both Filipinos, pleaded guilty to operating a ship in a dangerous manner and attempting to pervert the course of justice by altering navigation records after the accident, Maritime New Zealand (MNZ) said.

At a hearing in the Tauranga District Court, the captain also admitted discharging harmful substances from the cargo vessel, MNZ said.

It said the men, whose names have been suppressed since they were released on bail last year over fears for their safety, could face lengthy jail terms. They will be sentenced on May 25.

The Rena hit the Astrolabe Reef 22 kilometres (14 miles) offshore in clear conditions as it steamed at full speed towards Tauranga, New Zealand's largest container port, becoming stuck fast on the submerged rocks.

More than 300 tonnes of toxic fuel oil spewed from the vessel, creating an oil slick kilometres (miles) long, which washed onto beaches at the popular tourist spot, coating birds in thick black sludge.

Environment Minister Nick Smith described it as New Zealand's worst maritime pollution disaster and claimed shortly after the accident that the Rena hit the reef while taking a short cut to reach port.

The disaster triggered a dangerous salvage operation which involved crews scrambling to pump remaining oil from the Rena's fuel tanks as heavy seas pounded the stricken vessel, opening up deep cracks in its hull.

An army of 5,000 volunteers was also mobilised to clean up the shoreline of the bay, which contains marine reserves and teems with wildlife including whales, dolphins, penguins, seals and rare sea birds.

MNZ said this week that clean-up teams had removed more than a cubic kilometre (0.24 cubic miles) of waste such as polluted sand and soil from the shoreline.

The vessel eventually broke up on the reef in January, when the stern sank, further complicating a salvage operation which is still continuing after five months as crews remove shipping containers from the bow.

Earlier this month, Smith estimated the disaster clean-up cost would total NZ$130 million ($110 million), most of which would be covered by its owner, the Greece-based Costamare Shipping Company,

Prime Minister John Key said the guilty pleas vindicated the charges.

"It's important justice (is) bought to bear here," he told Fairfax Media.

"Significant environmental damage (has) occurred in New Zealand and the government is very concerned about that."

In total, the captain pleaded guilty to four criminal charges and the second officer to three. Each of the charges carries a maximum penalty of seven years' jail.

The charge of operating a ship in a dangerous manner can attract a one-year jail term, while the maximum sentence for discharging harmful substances is two years or a NZ$300,000 ($252,000) fine.