The company has applied to use the Abel Tasman to buy and process fish, instead of trawling to fulfil its quota for jack mackerel and red bait.
Authority spokesman Dr James Findlay says there is concern the transfer of fish could pose a risk to other species.
He says the quota system is another issue.
"This is a quota managed fishery and we need to ensure the integrity of the quota managed arrangements which mean we have a robust way of measuring the amount of fish that are being caught by which vessel because that's how we attribute the quota," he said.
"This may make more difficult that process, but we also may have ways to get around that."
In a previous statement, Seafish director Gerry Geen says transferring fish between ships has happened many times before in the small pelagic fishery.