Environmental groups claim shark finning in Northern Territory waters is being carried out by boats operating out of Darwin Harbour.

The Territory Environment Centre and the Australian Maritime Conservation Society says the carcasses minus their fins are being sold as fertiliser for a pittance.

"There're boats that are going out targeting shark fins, which doesn't occur anywhere else in Australia," said spokeswoman Adele Pedder.

"When you see that they come onto land and are sold to fertiliser factories for 25 cents a kilo, that's just a very wasteful practice."

Ms Pedder, who works for both organisations, says the Territory Government has regulated to stop the dumping of carcasses at sea after the fins are removed, but it must do more.

She says the Government must follow other jurisdictions and stop shark finning altogether.

"Our sharks in Australia are a valuable resource, and especially in the Northern Territory where we have one of the most diverse shark faunas in Australia," she said.

"We need to recognise that, place more value on the sharks, ban shark finning."