A unique species of killer whale is disappearing from the Ross Sea, and New Zealand's Antarctic deep-sea fishing may be partly to blame.

A group of Italian and American researchers who visit Antarctica yearly have noticed a large drop in the number of killer whales, or orca, since 2002.

Sightings dropped from a high of 120 orca at one time in 2002-03 to 18 at one time last summer, and the number of days on which orca were spotted fell by about half.

The researchers, who published their work in the journal Aquatic Mammals, believe the change is linked to the rise of a multimillion trade in Antarctic toothfish, led by New Zealand and Korea.

But the body in charge of managing Ross Sea toothfish boats, the Commission for the Conservation of Antarctic Marine Living Resources, says too little is known to say whether fishing is harming the orca.

"We don't have the information to say that it isn't or that it is," said the commission's executive secretary Denzil Miller.

Ross Sea orcas are a sub-species of killer whale, and have different DNA to those found elsewhere.

They hunt toothfish and other fish in the Ross Sea, sometimes following paths made by ice breakers.

Dr Miller said orcas would eat scraps from the fishing boats, regarding them as a "cheap and cheerful takeaway meal".

"Orcas interact with the fishery, that is the bottom line, but we don't know what the consequences of that interaction are."

But the researchers believe there is a link with fishing. They said scientists on the ice had struggled to find toothfish to tag and release in recent years.

Antarctic toothfish can live up to 40 years, are more than 1.5m long and live as deep as 2km. They are sold to restaurants in the United States as Chilean sea bass, and are seldom available in New Zealand.

Dr Miller did not doubt researchers had observed changes in orca behaviour and found fewer toothfish near the research base.

"What is very difficult to know is whether there is a cause and effect. There have been some environment changes in the area ... for example changes in the ice," he said.

He said the fishery was strictly controlled. But the exact proportion of fish being caught is not known.

Supporters of the fishing trade say scientists would know little about the Ross Sea toothfish without scientific observers who are carried there by fishing boats.

But opponents say the Antarctic living resources conservation commission is allowing the eco-system to be exploited simply to save member countries money on Ross Sea research.

Paper author Dr David Ainley and a fellow ecologist Peter Wilson toured New Zealand last year asking people to back efforts to end Ross Sea fishing.

The toothfish catch peaked in 2001, and New Zealand's share is worth between $20 million and $30 million a year.