Marine scientists say they have found evidence of the role sharks play in reef environments, with declining shark populations linked to damage on coral reefs.

Dr Mark Meekan from the Australian Institute of Marine Science led a team of Canadian and local researchers in a study of coral reefs about 300 kilometres off the north-west Australian coast.

He says Indonesian fishermen from places like Rote in West Timor travel to the reefs every winter to catch sharks, and their hunt has a dramatic effect on the population of reef sharks like the hammerhead and whaler.

"They are still allowed to do it using the same traditional methods, that is, these little sailing canoes, these little dug-outs," he said.

"The funny thing is that although these guys are just in sailing canoes and putting out long lines, they're very effective at removing sharks.

"The reefs where they're allowed to go, we've basically found that they've wiped out pretty much most of the sharks that used to be there.

"And that's had some very interesting impacts on the rest of the fish communities."

Dr Meekan says smaller predatory fish - such as emperors and snappers - are more abundant on the reefs without sharks than those where no fishing takes place.

"You might think that's a really good thing but unfortunately, the effects haven't stopped there," he said.

"They've flowed right down the food chain and now they're affecting things like the algae-eating fish that are further on down the food chain on the reef."

He says natural disturbances such as cyclones and bleaching kill off live coral, and the ecosystem does not recover in the same way if the food chain has been disrupted.

"Algae grows on the reefs as the coral dies," he said.

"The herbivores - these algae-eating fish - are very important because what happens is they clear a bit of space in that algae and allow the coral areas to regrow.

"Now if there aren't enough algae-eating fish out there, that could be a real problem for the recovery of reef from these types of disturbances."

Dr Meekan says it is critical to protect sharks.

"Coral reefs face a very uncertain future, but there is something we can do about protecting reef sharks," he said.

"A lot of these animals are very resident on reefs, they don't go very far.

"So even by creating small marine parks that protect these animals, we are in actual fact increasing a resilience to these reefs, and we're creating some hope for the future."

The research is being published in the journal PLOS ONE.