"To safely free the log, the only option available was to cut a hole in the net to release the log.
"Unfortunately this has meant there was a small amount of fish lost at sea," Mr Carrington said.
Whangarei man Darren Shields was out spearfishing on Friday about 8am.
"They were all around the area ... hundreds of them floating in the water," Mr Shields, who has been visiting the islands for the past 30 years, said. He contacted the ministry immediately.
Mr Shields' vessel brought home 35 fish that had been floating in an area about quarter the size of a rugby field.
"We have all had a hand in taking fish from the sea. But when you see a thing like this, it's a shocking waste."
Mr Carrington said the commercial vessel's skipper had tried to collect as many fish as possible in the dark on Thursday, and had reported an accidental loss of fish to MPI.
"He (the skipper) followed correct procedure at all times."
Aotearoa Fisheries did not condone the dumping of fish and ensured all contracted fishers had sufficient access to quota so there was no need for dumping or high-grading.
Ministry compliance director Dean Baigent said it would investigate.
The recreational fishers had done "everything right".
"Getting accurate information about something happening on the water meant we could respond immediately," Mr Baigent said. "We chartered a plane from Ardmore and got out to the scene and recorded six commercial boats in the area and recorded their positions."
He said the aircraft did not find the slick of fish, but had been given photos and specimens collected by recreational fishers.
Crew from five commercial boats which were in the area will be interviewed as part of the investigation.
