The Rena is now in two parts in heavy seas off the coast of Tauranga.
Container recovery company Braemar Howells estimated between 200 and 300 containers were lost from Rena after it split apart and shipping warnings have been issued.
The ship is in two sections on the Astrolabe reef about 20 - 30 metres apart. It went aground there on 5 October.
Environment Minister Nick Smith says the stern is likely to sink and the latest developments are serious but not unexpected.
He says the environmental risks associated with the Rena are now a fraction of what they were when the ship ran aground because the majority of heavy fuel oil on board was removed.
Dr Smith says it's unlikely any beaches will be closed as a result of oil leaking from the Rena.
Braemar Howells says about 20% of the boxes that have fallen overboard will float and the rest will sink.
Acting operations manager Claudene Sharp says about 30 containers from the ship have already been identified.
She says those that have already been located would be collected once the sea state improved.
Ms Sharp says a sonar equipped vessel was searching for the other containers and the priority was to ensure that the shipping lanes remained clear.
She says on Sunday the containers were moving in a westerly direction between Astrolabe Reef and Mayor Island and warned they could come ashore along the Bay of Plenty coastline over the next 24 hours.
There were more than 1300 containers on board the Rena when it hit the Astrolabe Reef and around 830 containers remaining prior to those lost on Sunday.
Some oil has already been spotted leaking from the ship and is expected to wash up on eastern beaches on Monday.
The Rena was pounded by swells of up to six metres overnight and more severe weather is expected for the next three to four days.
Maritime New Zealand says the front section of the wreck is in its original position, but the stern section has broken away and is moving significantly on the reef.
The high seas wrenched hatch covers off the vessel, releasing containers from the hold.
Navigational warnings have been issued for shipping.
Maritime NZ says there is a large debris trail around the vessel.
Bay of Plenty Regional Council says it is likely a three mile exclusion zone around the ship will be extended.
Maritime NZ says a response team has been activated to respond to any more oil released from the ship.
The Port of Tauranga has also issued a warning to ships heading into the harbour to use extreme caution and maintain a vigilant lookout.
It says containers from the Rena have been spotted up to 10 nautical miles north of the port.
Ships awaiting entry to the port are advised to drift north of Mayor Island.