An ocean ecologist says he is extremely disappointed after he saw a commercial fishing boat allegedly longline fishing at the Poor Knights Islands Marine Reserve.

Glenn Edney, who also skippers a dive charter boat out of Tutukaka to the Poor Knights, off the east coast of Northland, said he saw the boat fishing around the islands on Tuesday.

Recreational and commercial fishing is restricted around the marine reserve, which extends 800m offshore around the islands.

The Fisheries Act prohibits longline fishing by commercial boats within 1 nautical mile (1.8km) of the islands. It also prohibits trawling within 3 nautical miles of the islands.

Mr Edney said he was snorkelling with a group of friends near the Riko Riko cave when he noticed the commercial fishing boat.

"It looked a little suspicious, I have to say, because they were pretty close in, and they did appear to be fishing," he said.

"These guys, according to my GPS and according to the other charter boat I called over to verify ... were somewhere around about 600-700m inside the 1 nautical mile exclusion zone for commercial fishing."

Mr Edney has laid a complaint with the Ministry for Primary Industries.

He said the Department of Conservation (DoC), which was tasked with taking care of marine reserves across New Zealand, did a "fantastic job".

However, he said DoC had have very few resources, and it was up to other people who used the marine reserve to keep an eye out.

Mr Edney was concerned about an increase in illegal fishing at Poor Knights.

"Unfortunately there have been very few prosecutions. It's difficult to get prosecutions and people are getting frustrated because of that."

Mr Edney has since posted a statement and photos of the alleged longline fishing boat to his Facebook page. The post has been shared over 700 times.

"I'm a little surprised at how viral the Facebook thing has gone - but it really indicates just how passionately people feel about not only the marine reserves, but also about not playing ball and fishing illegally."