Ministry for Primary Industries investigating thousands of dead fish in Auckland's Hauraki Gulf

The Ministry for Primary Industries (MPI) is investigating how thousands of dead, rotting fish have washed up on a Hauraki Gulf island.

Residents on Kawau Island noticed the decomposed Mackerel appearing on Thursday with no clues as to the cause.

A spokesperson for marine not-for-profit group LegaSea said the fish were "as far as you could see".

"Yesterday I went up the bank and had a quick fish and found a patch where they were every 20 or 30 feet," Scott Macindoe told Newshub.

"Quite incredible. I've never seen anything like it."

Macindoe estimates there are between 10 and 20 tonnes of them and he's "sent lots of calls to MPI".

"The locals are pretty uptight about it because they stink and we're having to pick them up," he said.

Initially thinking the fish came from a trawler, he's now not so sure.

"On this occasion, I'm beginning to think that there are too many of them for that event and it may well be something in the water," he said.

The Department of Conservation and Ministry for Primary Industries are looking into the event, according to Stuff.