Salvage crews have pumped almost all the oil from a container ship that ran aground on a New Zealand reef and caused the country's worst maritime pollution disaster, authorities said Monday.

Maritime New Zealand (MNZ) said only about 60 tonnes remained on the Rena and the focus of the salvage operation had shifted to removing shipping containers from the stricken vessel.

"While getting the bulk of the oil off the Rena is a significant milestone, our job isnt done yet," MNZ on-site commander Mick Courtnell said.

The Liberian-flagged ship was carrying 1,700 tonnes of oil when it ploughed into a reef on October 5, releasing about 350 tonnes into the North Island's pristine Bay of Plenty.

The resulting oil slick killed about 1,300 birds and fouled beaches in the popular tourist area with black sludge.

The Rena remains stranded on the reef with huge cracks in its hull and Matthew Watson, a spokesman for the salvage company working on the ship, said removing 1,200-plus containers from the badly listing vessel would take a long time.

"Getting those containers off is going to be a long, awkward, difficult process in itself, we're talking about months not weeks," he told Radio New Zealand.

"Then of course, beyond that, we're looking at how to try and get the Rena off the reef. That's assuming she doesn't break up in weather conditions in the interim."

The Rena's Filipino captain and second officer been charged with operating a vessel in a manner causing unnecessary danger or risk and discharging harmful substances.

New Zealand's Environment Minister Nick Smith has claimed the Rena hit the Astrolabe Reef while taking a short cut to reach port.