A haul of more than 60 shark fins, skins and flesh has been discovered on board an Indonesian fishing boat in waters off the coast of Darwin.

Key points: The boat was found two nautical miles inside Australian waters

The boat was found two nautical miles inside Australian waters Authorities found 63 fresh shark fins, 16 shark skins and 60 kilograms of shark flesh

Authorities found 63 fresh shark fins, 16 shark skins and 60 kilograms of shark flesh The boat was Indonesian with five crew members on board

The Australian Fisheries Management Authority (AFMA) said the boat was likely in the early stages of its fishing operation before it was apprehended 187 kilometres from Croker Island.

Peter Venslovas, AFMA's fishing operations general manager, said Australian Border Force officers found five crew on board with a suspected illegal catch of 63 fresh shark fins, 16 shark skins and 60 kilograms of shark flesh.

Despite the relatively small quantity found, Mr Venslovas told the NT Country Hour shark fin could fetch up to $175 per kilogram in Indonesia.

"Shark fin does fetch some fairly lucrative prices," he said.

"It's important that we send strong messages to those who feel they can come into Australian waters and target our fish stocks."

The boat was burnt yesterday morning after being escorted into Darwin Harbour to AFMA's vessel destruction facility.

"Because of the nature of them, destruction is the most effective method to deal with that quarantine risk," Mr Venslovas said.

More than 60 shark fins were found on board the suspected illegal fishing boat in waters near Croker Island. ( Supplied: Australian Border Force )

AFMA fisheries officers have started their investigation and will recommend charges to the Director of Public Prosecutions.

"The usual process is to charge the master, because the master is in charge of the vessel and he's the brains behind the operation," Mr Venslovas said.

Mr Venslovas said the maximum fine is $52,500 but the confiscation and destruction of the boat was the most significant financial penalty.

He said it was the second boat apprehended in Australia's northern waters this financial year — five were found last financial year.

"When boats do take their chances and have a crack at Australian waters, it's important that we're out there to apprehend them," he said.

According to AFMA, eight of the 36 boats found in waters north of the NT, Western Australia and Queensland in the last three and a half years had shark fin on board.

The most common species found were white tip and black tip reef sharks, tiger sharks, hammerhead sharks, whaler sharks and sandbar sharks.

