Spitzer Salvage spokesperson Matthew Watson said the stern section - which became about 75 per cent submerged when it slipped on the reef on January 8, was now about 97 percent underwater.
He told Radio New Zealand the vessel will be checked again today and may have slipped even further.
The 12m swells which have battered the ship in recent days had made the removal of containers "absolutely impossible".
"The salvors won't be going anywhere near the Rena while the swells are that large," Mr Watson said.
"We are at the mercy of mother nature."
The rough weather is expected to continue for several days.
Meanwhile, the Government is working on a law change to save taxpayers from the heavy cost of another large oil spill.
Under the Maritime Transport Act, ship owner Costamare is liable for up to $12.1 million - an amount that would have doubled to $24 million if New Zealand had signed up to the International Convention on Civil Liability for Bunker Oil Pollution Damage.
With the clean-up bill now sitting at $27.5 million, the Government is developing amendments to the act that will increase the cap for maritime claims against ship owners.
The Issues
The clean-up
At both ends of the Bay of Plenty, the job of cleaning up the Rena's mess drags on. In recent weeks, clean-up teams have retrieved debris at Ohope, Whakatane, near Katikati and Waihi Beach, and often-hit Motiti Island. Debris had been found as far north as the Coromandel and far east as Gisborne.
Yesterday, Tauranga City Council said it had found a novel use for some of the timber sleepers - the city's new waterfront development. Although all but the dregs of the Rena's oil supply have been pumped off, fresh reports of oil continue.
The salvage Removal of the Rena's heavy oil was effectively completed in November - a month before a ferocious storm finally split the ship in half.
Since January 8, when the stern section slipped almost entirely under water, a 25-strong team of international salvors have been fighting an increasingly perilous battle to remove containers and debris.
Over recent weeks, salvors had pulled containers and their remains from the ship and collected debris from the seafloor in what Svitzer Salvage spokesman Matt Watson called an operation that remained "minute by minute, hour by hour, day by day".
"There's really no such thing as a finish line. This mission every day is to do what's possible and get more debris off."
Salvors have so far removed 584 containers, but about 250 remain below decks in the severed bow and an unknown number are submerged inside the stern.
The investigations
An interim Transport Accident Investigation Commission report, released last month, has revealed how the Rena's crew cut corners on the way to the Port of Tauranga - but it stopped short of casting blame.
A final report covering why the accident happened is due out next year.
Maritime NZ said issues such as compulsory shipping lanes were matters for consideration further down the track.
Transport Minister Gerry Brownlee said it was too early to consider prescribed navigation routes, but added that New Zealand had low levels of shipping traffic by international standards.
Maritime NZ is conducting its own review which is likely to look at the agency's use of volunteers, its response to the threat to wildlife and whether its equipment was adequate.
Court cases
Cases against the Rena's captain and navigation officer are due to be concluded next month. Both men have pleaded guilty to a charge under section 65 of the Maritime Transport Act in relation to operating a ship in a manner causing unnecessary danger or risk to persons or property.
The captain has admitted a charge under the Resource Management Act of being the master of a ship from which harmful substances or contaminants were discharged into the coastal marine area, and also to four charges under the Crimes Act of wilfully attempting to pervert the course of justice.
The second officer has pleaded guilty to three similar charges, which relate to altering ship documents after the grounding. He is yet to answer a charge under the Resource Management Act relating to the discharge of harmful substances and/or contaminants. His lawyer confirmed the officer intended to plead guilty.
Both will appear again for sentencing on May 25.
Each charge under the Crimes Act carries a maximum penalty of seven years' imprisonment, the Maritime Transport Act charges have a maximum fine of $10,000 or 12 months' prison, while the Resource Management Act charges carry a maximum $300,000 fine or two years' prison and $10,000 for every day the offending continues.
Action against owners
The Government refuses to shed any light on legal negotiations with Costamare.
If the Government successfully prosecuted Costamare under the Resource Management Act, the company could be ordered to pay a $600,000 fine, with an additional $10,000 fine for each day the offending continued.
The economic costAbout 20 businesses, groups and individuals being co-ordinated by Nevan Lancaster, whose kayakhire business lost more than $5000from the disaster, plan to have legal representation organised by April 20 to launch a class action against Costamare.
Potential losses to Tauranga businesses from the Rena have been put at $1.2 million a day.
About 55 per cent of operators said they were negatively affected by the disaster and 70 per cent reported that business was down over the holiday period.
The environmental cost
The media was full of images of dirty beaches, oiled birds, and volunteer attempts to clean them. The immediate effects have passed, but long-term effects have yet to be seen.
Maritime NZ national on-scene commander Rob Service said he was not aware of any ongoing or long-term effect on the environment. Once cleaned from the coastline, the oil had "pretty well been removed".
A $3 million multi-agency environmental recovery plan had a year-long timeframe and will be extended in September if needed. A website will soon give updates on key areas.
