The report by the University's Business School included interviews with crew members of the South Korean fishing trawler Oyang 70 which sank with the loss of six lives in August last year, and its replacement vessel the Oyang 75.
Its survey of industry insiders and more than 100 crew members found workers were regularly exploited by fishing companies and the agents who hired them, and that New Zealand officials were routinely lied to about wages and conditions.
Researcher Dr Christina Stringer told Radio New Zealand the Indonesian crew of the Oyang 75 told her of being beaten, working 40 hour shifts until they begged for a break, and sexually abused.
Some workers were given fish bait for their meals, she said.
The company at the centre of most of the allegations, Sajo Oyang Corporation, has rejected the claims describing them as "bizarre".
The Service and Food Workers Union, which represents 2000 seafood workers, said the shameless exploitation of foreign crews needed urgent attention.
But its spokesman Neville Donaldson said the loss of thousands of land-based jobs also needed to be canvassed.
"As long as quota owners can hand over our fishing industry to foreign companies and foreign crews and as long as our seafood industry can ship New Zealand's seafood resource to China for processing, New Zealanders will miss out on desperately needed jobs, career paths and maximum economic return for our fish products."
He said the investigation was critical for Maori workers, who have traditionally made up a large percentage of the seafood industry workforce.
Ms Wilkinson said the rules governing the fishing industry could change if the inquiry finds it has not been living up to Government principles.
"This panel has considerable experience. Should they find that government's objectives are being undermined by current practice, it is expected that they will make recommendations relating to policy and legislative amendments, and suggest improvements to operational practices."
The inquiry is set to be chaired by Paul Swain, a previous Minister of Labour and Immigration.