"The alleged abuse is against predominantly Indonesian crew members," the report said.
The report found that the way some foreign-flagged FCVs were operating had "the potential to damage New Zealand's international standing and harm the fishing industry's reputation".
The Government had also been criticised for the weakness of its monitoring and enforcement regime, the report said.
In particular, New Zealand's seafood industry was at risk, a number of companies noting retailers in markets such as Britain paid close attention to customers' ethical considerations around the foods they bought.
"The recommendations include updating the Code of Practice and strengthening the immigration approval process - both of which will help ensure better conditions for workers on FCVs," Ms Wilkinson said.
"We will also be adopting a recommendation that the New Zealand fishing companies chartering foreign vessels have to show the code is being followed."
Ms Wilkinson said the move would put the onus on the companies rather than the Department of Labour, which currently had to prove code breaches.
Among the recommended law changes were Fisheries Act amendments that would give explicit power to revoke FCV registration if information received warranted reconsideration of the initial consent. Maritime Rules could also be revised to ensure they applied to FCVs as well as New Zealand ships.
Mr Carter said the Government would analyse the economic effects of the recommendations but he didn't believe they would impact severely on reputable operators.
"And if they're not reputable, frankly I don't want those operators in New Zealand waters," he said.
Green Party fishing spokesman Steffan Browning was disappointed with the Government's response, saying accepting only six of the 15 recommendations wasn't good enough and all of them should be adopted.
"[Our] overseas reputation as a country with good labour practices has been found severely wanting. Overseas media have picked up on the slave labour practices on boats working in our economic zone."
TAKEN ON BOARD
* Place observers on all FCVs fishing in the exclusive economic zone.
* Consider non-fisheries offences when making FCV registration decisions.
* Introduce a safety system to help clearly identify an NZ party that can be held accountable for breaches.
* Tighten a code of practice on foreign fishing crews.
* Increase frequency and thoroughness of inspections.
* Closer inter-agency co-operation to improve worker conditions.