The company recently applied to use the Abel Tasman as a floating freezer, to buy and process fish, instead of trawling.
It put forward the compromise after the Minister banned it from trawling for two years.
Mr Burke has told Lateline he had received the environmental impact study and he was not satisfied with the new proposal.
"Even though it sounds like, oh, they're not putting the net out, there's no problem," he said.
"The advice that came back, for seals and dolphins and localised depletion, the problems that arise are exactly the same.
"For seabirds, the problems are potentially worse."