Aboard the Chinese long-liner, around 15km from land, the hold contained a sizeable catch of albacore and yellowfin tuna, matching the captain's books.
The vessel had about 80 tonnes of fish aboard, and the documentation appeared to be in order, NZ navy officials said. But the vessel had been at sea for more than a month and there was no presence of rubbish aboard.
NZ navy officials allege that rubbish had simply been disposed of into the ocean.
Dumping rubbish can attract a fine of up to $500,000 and it could impact their ability to get a future licence, the NZ navy said.