The stern section of a stricken cargo ship is slipping off a New Zealand reef where it has been stuck for three months and is in danger of sinking, authorities said, complicating salvage efforts in one of the nation's worst environmental disasters.

The rear section of the 47,230-tonne Liberian-flagged Rena, had moved to the edge of the reef, about 22 km off Tauranga on the east coast of New Zealand, where it has been wedged since early October, and is almost totally under water.

"The foremost part of the stern was still sticking up out of the water, with the rest - including the bridge - submerged," Maritime NZ said in a statement today.

A tug has a line attached to the stern to stop it drifting into shipping lanes. The water around the sinking section is up to 30 metres deep, which experts have said previously would make salvage operations more difficult,

The bow section of the 236-metre ship is still upright and wedged on the reef.

The Rena finally broke in two on Sunday after being pounded by waves of up to 6 metres, spewing more oil and more than a hundred containers into the sea.

Maritime authorities and salvage crews had removed most of the thick, toxic fuel oil and nearly 400 containers from the ship, which ran aground in calm conditions on Oct 5. But fuel and cargo have continued to leak in rough seas, causing New Zealand's worst environmental disaster in decades.

A large amount of cargo - timber, plastic, and bags of milk powder - has washed up on beaches as far as 60 km from the ship, and more than 20 containers have washed up on a nearby island.

Some have been tagged with transponders and the New Zealand navy is scanning the area with sonar to ensure nearby commercial operations at the Port of Tauranga, the country's biggest export port, are not interrupted.

Thousands of birds were killed by the earlier spill and it has taken months to clean up the shore in an area popular with holiday makers and surfers .

The Rena's captain and navigation officer, both Philippine nationals, have been charged with operating a vessel in a dangerous manner, and releasing toxic substances, which carries a maximum fine of NZ$300,000 ($230,500), or two years in prison.

They also face charges of attempting to pervert justice by allegedly altering documents after the grounding.

They are due to appear in court again next month.

The vessel is owned by Daina Shipping, a unit of Greece's Costamare Inc and was under charter to Mediterranean Shipping.

Heavy machinery moves shipping containers that came ashore from the stricken ship ( AAP/NZN/SNPA: Ross Setford )

Reuters