Three illegal fishing vessels apprehended in Western Australia's far northern waters have been seized and destroyed along with an enormous haul of illegally caught seafood, border protection officials have confirmed.

Earlier this week the ABC reported the discovery of four fishing vessels in the remote mangroves at Kuri Bay, 220km north of Derby, by traditional owners and a local tour operator.

In a statement released on Thursday, the Australian Border Force (ABF) confirmed three of the four vessels had been destroyed at sea.

The haul included 700 kilograms of sea cucumber, 2,450kg of salt, 4kg of shark fin, 4kg of sea urchin and a large amount of fishing equipment.

Sea cucumber is considered a delicacy in Asia and can sell for hundreds of dollars per kilogram.

Thirteen of the 33 fishermen apprehended were returned to sea on the fourth vessel, which was taken out of Australia's territorial waters.

The remaining 20 will be transferred to the mainland for investigation of suspected fisheries offences.

News of the discovery of the boats was met with frustration and questions about the ABF's capacity to monitor WA's vast northern coastline.

According to the Australian Fisheries Management Authority (AFMA), 216 foreign fishing boats were intercepted between July 1, 2023 and April this year, compared to 125 in the previous financial year.

In a 2022 statement AFMA noted the sharp rise in Indonesian fishing vessels in Australian waters was a symptom of an economic downturn in Australia's nearest neighbour.

"This increase in illegal fishing is attributable to social and economic pressures on Indonesian fishers as a result of the pandemic, among various other factors, including the high market value for some species, such as sea cucumber," the statement read.

Sea cucumber, or trepang, are invertebrate animals that creep along the sea floor to feed and are a delicacy in South-East Asia.

Sustainability fears

Scientists are warning of the threats posed by illegal foreign fishing to the sensitive Kimberley coastline, in and out of the water.

Anthony Hart has spent more than two decades researching the sustainability of sea cucumber stocks, which he says are vulnerable.

WA has the only certified sustainable sea cucumber industry in the world and he warned unregulated foreign fishing jeopardised this status.

"Because sea cucumbers are found in shallow water areas in quite high densities, it's just very easy for a boat to hit on the sea cucumber patch and, within a day or two, knock it down to … low levels," Dr Hart said.

Dr Hart works for Tasmania Seafood, which owns most sea cucumber licenses in WA and the NT.

The company recently pulled its boats out of Kimberley waters due to concern about stocks.

"We resolved after a recent assessment we had to stop fishing there until we had more information," Dr Hart said.

"But we have our licenses to fish, which we've bought on the open market.

Concerns for country

It is not just marine scientists who are concerned about illegal fishing.

Larissa Potter is a senior field ecologist with the Australian Wildlife Conservancy and, along with the Dambimangari Aboriginal community, has been surveying the biodiversity of the islands north of Broome.

She is worried foreign fishing boats are creating a biosecurity risk.

"There's risks of diseases, and mostly [what] I'd be more concerned about is introduced species, if they've got something on the boat, like black rats or a cat," Ms Potter said.

In a statement, an ABF spokesperson said Operation Leedstrum ensured an "increased patrol and response capability in far north-west Australia".

"[This includes] increased staffing, patrol vehicles and a rotary wing asset for rapid response to any BorderWatch reporting from members of the public," they said.

"The operational response is ongoing and ABF will not comment any further than to say ABF/Maritime Border Command pursues strong enforcement action in cases of illegal foreign fishing, in consultation with AFMA."