A cargo ship that caused New Zealand's worst maritime pollution disaster when it ran aground three months ago broke in two in a storm on Sunday, raising fears of a fresh environmental crisis.

A team of oil-spill and wildlife specialists has been mobilised as oil again began flowing from the Rena which has been stuck on Astrolabe Reef off the North Island resort area of Tauranga since October 5.

Shipping was also being warned away as up to 300 containers were washed from the wreck and salvage workers said there was a strong likelihood the stern section would capsize.

The Rena is now in two pieces which have been forced 20-30 metres (yards) apart after being pounded by waves up to seven metres high.

Maritime New Zealand (MNZ) on-scene commander Alex van Wijngaarden said the National Response Team, which included oil spill response and wildlife experts was preparing for the likelihood of more oil coming ashore.

"While it is unknown at this stage exactly how much oil may be released, teams have been mobilised and will be ready to respond to anything that may come ashore," he said.

"The wildlife response had also been increased to help deal with any affected wildlife."

When the Rena ran aground, about 350 tonnes of oil spilled into the sea and was washed on to once-pristine beaches, killing at least 1,300 birds while an army of volunteers combed the coastline and saved hundreds more.

More than 1,000 tonnes of oil have since been pumped off the ship but there is more on board and while it posed a risk Environment Minister Nick Smith said it would not be as bad as when the Rena first ran aground.

"At the most tens of tonnes of oil rather than hundreds of tonnes that potentially could be spilled," he said.

Salvors have also been removing containers from the vessel and said before the storm hit there were an estimated 881 still on board. Only a few of the ship's original consignment of containers had hazardous cargo.

Container recovery specialist Claudine Sharpe said "between 200 to 300 containers" were washed overboard as the ship separated and only about 40 to 60 would have remained afloat.

MNZ salvage unit manager David Billington expected more containers to be lost before the storm eased in about three days as both sections of the ship were open to the sea and vulnerable to more damage.

"While the two sections of the Rena currently remain on the reef, there's no question the ship is badly damaged with the severe movement breaking off many of the hatch covers and releasing containers from the holds," he said.

MNZ salvage advisor Jon Walker said the stern section, listing at 24 degrees, was likely to capsize and sink which would make recovering further containers from that section considerably more difficult.

Attempts were being made to tag the containers in the water as it was too rough to tow or recover them and a navigational warning had been issued to shipping.

The regional harbour master was also considering extending the three nautical mile exclusion zone set up around the Rena because of the large field of debris flowing from the ship.

The Filipino captain and second officer of the Rena have been arrested and face multiple charges over the grounding, including operating a vessel in a manner causing unnecessary danger or risk.

They have also been charged with attempting to pervert the course of justice, which carries a seven-year jail term, amid accusations documents were altered after the grounding.

The two men are on bail but are being housed at a secret location for their own safety because of fears of a public backlash

Environment Minister Smith has claimed the Rena hit the Astrolabe Reef while taking a short cut to reach port.