New university research compiled from interviews with dozens of fishermen has exposed disturbing levels of inhumane treatment on foreign fishing vessels operating in New Zealand's exclusive economic zone.

The conditions suffered by 2000 mainly Indonesian men on 27 vessels were judged "appalling", with gruesome accounts of extreme physical violence and verbal abuse.

"Officers are vicious bastards ... factory manager just rapped this 12kg stainless steel pan over his head, splits the top of his head, blood pissing out everywhere...," one informant told the University of Auckland.

"I told the Master can't leave him cause he's bleeding all over the squid. He said 'Oh no no, he's Indonesian, no touchy no touchy'... Took him to the bridge and third mate said 'Indonesian, no stitchy no stitchy'. I ended up giving over 26 stitches ... bit of a mess."

Muslim workers were frequently called dogs, monkeys and other derogatory names.

Others were sexually abused, one describing being forced to "massage" the captain every day.

Another said: "Galley boy, good looking boy on a Korean boat was raped by four Chinese crew who got him...."

They drank brown water, ate rotten fish bait and were denied medical treatment when sick or injured.

A fisherman described his experience as being "trapped into modern slavery", while another said they lived "like rats".

A New Zealand official quoted in the study called the boats "a floating freezer ... absolutely appalling conditions just like a slum ... there are definitely human rights abuses out there, they are slave ships".

Many of the interviewees were survivors from the 30-year-old Oyang 70, which sank off New Zealand's South Island last year, killing six men.

The replacement crew and crew from another boat, the 30-year-old Shin Ji, have also contributed after marching off the job objecting to poor conditions and wages.

The Korean company at the centre of the allegations, Sajo Oyang Corporation, has denied claims of widespread abuse. In a statement, it said it had not been asked to offer evidence and claimed the researchers were known to be against foreign fishing.

The study, entitled "Not in New Zealand's waters, surely?", showed the men's annual incomes were just a tenth of what crew on New Zealand boats received. Many did not get one day off in two years, and worked an average of 16 hours a day.

However, falsified time sheets showed shorter days and regular breaks.

Paperwork obtained by the researchers show New Zealand officials were routinely and systematically lied to over wages and conditions.

The revelations have shocked New Zealanders and sparked a ministerial investigation into the operations.

The crew of both boats remain on New Zealand shores fighting for lost wages.

Immigration officials had planned to deport them but this is unlikely to go ahead amid fears the company may never pay the men and may seek retribution upon return to their homeland.

"Deporting the men now would be unjust and also prevent all the relevant evidence being available to the ministerial inquiry into the conditions on foreign charter fishing boats in New Zealand waters," Green Party MP Keith Locke said.