Two women from Perth, who were snorkelling at Ningaloo Reef in Western Australia have described the terrifying moment a fellow swimmer was crushed by a humpback whale.

Speaking to The West Australian, Tahnee Pitman and her friend Sharnee Pannell had just finished their second snorkelling expedition when the mammal struck a 29-year-old woman, which left her with internal bleeding and broken ribs.

Pitman, who had seen the whale while swimming around the reef, said the mother and her calf became "protective" and "aggressive" towards the snorkellers in the water.

"They circled the group multiple times and became quite aggressive in their behaviour," Pitman told the publication.

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"(They were) swimming through the group with force and flicking their tails out of the water and swiping at swimmers. Instead of just swimming past the group of swimmers as usual, the whale and calf then swam directly up to the group and became very protective."

The woman who was struck by the whale wasn't the only casualty on the day, which tour operators have labelled as a "freak accident".

While the 29-year-old suffered fractured ribs and internal bleeding after the incident near Exmouth, another man was reportedly flung from the water by the 15-metre whale.

"We were all in shock, I really thought it was going to end a lot worse than it did," Pitman said.

Tahnee Pitman,left, and Sharnee Pannell were swimming in Western Australia on Saturday when the incident happened. Photo / Tahnee Pitman, Facebook.com
Tahnee Pitman,left, and Sharnee Pannell were swimming in Western Australia on Saturday when the incident happened. Photo / Tahnee Pitman, Facebook.com

"I was with a friend (Pannell) and we all just kind of sat in silence waiting for the ambulance to come on board as there was nothing we could do to help the injured. She (the injured woman) was in a lot of pain."

The injured woman – who is reportedly from the UK – was flown to the Royal Perth Hospital where she is in the State Trauma Unit in a serious but stable condition.

Matt Winter, a spokesman for the tour operators Ningaloo Whaleshark Swim, said the Department of Parks and Wildlife was investigating the incident.

He said the company had "fairly exhaustively" reviewed protocols and believed they had been properly followed.

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"As far as we can tell it's a freak accident," Mr Winter told NCA NewsWire.

"It's just one of those things that happens with wild animals in the ocean."

He said the woman was pinned between a young whale, which was a calf last year but is now quite large, and its mother.

Mr Winter said the mother may have been overprotective.

"It could have been freaked out by other whales in the area … orcas … we just don't know."

Pitman said the accident was handled "exceptionally well" by the crew, given the unusual nature of the incident.

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"No one had seen anything like it before in all the years they've been doing this so the crew were in as much shock as the rest of us," she said.