Intense marine heatwaves have destroyed some 400-year-old ancient corals off the Pilbara coastline of Western Australia.

The unusual heat events, which occurred in 2010-11 and 2012-13, seriously altered large reefs of staghorn and table corals stretching from the World Heritage-listed Ningaloo Marine Park to the Montebello Islands and the Dampier Archipelago. Some died, while the others were severely damaged.

"They are very robust and that's how they can live to be so old," Russ Babcock, CSIRO's lead scientist for the joint survey with the University of Western Australia, said. "Very few environmental events can affect them, let alone kill them."

He theorised that some of the corals had been experiencing severe bleaching over the past couple of years.

"We suspect this bleaching event was due to marine heatwaves that occurred in the region over the past few summers, and to see it up close was sobering," Mr Babcock said.

A separate research suggested the reefs became more susceptible to damage from the time it got hit by the first marine heatwave.

The first heatwave in 2010-11, according to Ming Feng, a CSIRO oceanographer, was due to the powerful La Nina event in the Pacific. The ever present climate change threat exacerbated the situation and made the corals more vulnerable.

"We also found there had been more recent bleaching in parts of that area which had occurred in 2013 and it looked that some of the effects were even more extreme than 2011 in that region at least," Mr Babcock said.

"It was strong enough that it seems to have affected some of these massive Porites corals, which form boulders that are up to four metres or so in diameter."

Mr Feng noted the water temperatures off the WA coast and the western Pacific are now "much higher than in previous decades." The 2010-11 marine heatwave alone spurred sea temperatures to rise 5 degrees above normal at their peak.

"As we continue to get warmer, any moderate La Nina event will cause a similar kind of heatwave effect, compared with a more severe event in the past," he said.