The federal government has been warned its plan to alter the boundaries of national marine parks could threaten the health of WA's prized Ningaloo Reef.

A draft rezoning plan for waters surrounding the reef would reduce the protected area 73 per cent, according to the Director of the School of Biological Sciences at the University of Western Australia.

Professor Jessica Meeuwig told radio 6PR the plans were "so below any scientifically supported standards [they're] basically a paper park."

Ningaloo Reef is protected under WA state law but there is concern opening up adjacent waters to commercial and recreational fishing, oil and gas exploration and the potential for deep sea mining will affect marine life.

"These places are connected, the fish don't say 'oh, I'm in state waters or 'oh I'm in federal waters," Prof Meeuwig said.

"For long ocean term health, resilience and stability it has implications that the federal government is proposing to gut that marine park."

The draft promises to increase the total area of marine parks open to fishing from 64 to 80 per cent, leading to 97 per cent of Australian waters within 100km of the coast open to recreational fishing.

AAP