The Maritime Union says an exemption for Japanese tuna fishers and some iwi quota holders in the Fisheries Amendment Bill should be thrown out.
It says last-minute changes to the bill by the Primary Production Select Committee would allow some iwi quota holders to sidestep the requirement to use New Zealand flagged vessels by 2016.
Maritime Union national secretary Joe Fleetwood says after years of deaths, injuries, abuse and criminal activity involving foreign charter vessels, the industry has to be cleaned up, with no exceptions - as was agreed.
Mr Fleetwood says the changes amount to the Government condoning slave labour.
"We'll just give everyone an exemption and be done with it. And let's just say, 'Yes, we accept ships of shame.
"We accept exploitation in the New Zealand fishing industry and New Zealand waters', and be done with it. Because that's what the Government's saying."
The union has called for the current 2016 deadline to re-flag foreign charter vessels to be brought forward to 2014.