The skipper managed to get the boat back to the Narooma boat ramp where he and his 18-year-old passenger were met by paramedics.

The teen was airlifted to Canberra hospital with serious head injuries and a suspected fracture to his neck.

The skipper was treated at Moruya Hospital for a suspected concussion and cuts on his face.

'It blows my mind'

John Moore, a former Montague Island charter operator, said the accident was very unusual.

"I'm extremely surprised — situations like this are very, very rare,' he said.

"Whales are incredibly intelligent, and very aware of the areas that's around them.

"From my experience, it's been a case of larger boats hitting whales and not large whales hitting small boats.

"It's incredibly rare for a whale to breach and land on top of a boat.

"In my 40-odd years at sea, I've only ever heard of it once before."

'Very unpredictable'

Superintendent Joe McNulty said Maritime NSW had launched an investigation into the incident.

"While inquiries are in their infancy, the incident demonstrates the dangers these mammals can pose to those on the water," the Marine Area Commander said.

"We encourage anyone hoping to get a closer look to maintain a safe distance.

"You must not approach a whale any closer than 100 metres on a vessel, including boats, surf skis and kayaks."

The Australian vice-president of the Organisation for the Rescue and Research of Cetaceans (ORRCA), Jools Farrell, said the incident highlighted the need to stick to the rules.

"It has happened in the past — whales can be very unpredictable," she said.

"That is why there are legal distances that people do need to stay away while in boats."

'A lot more out there'

Authorities believe the whale may have been injured in the collision and NSW National Parks and Wildlife Service (NPWS) and ORRCA will provide assistance if they can.

"We will be on the lookout for reports from the area," Ms Farrell said.

"I presume there may be some injuries, but it depends on the size of the whale as well.

"But fingers crossed the injuries to the whale aren't too severe.

"But our thoughts are also with the people that were on the vessel and were injured."

The size and species of the animal are not known, but the majority of whales heading north at this time of year are humpbacks.

Anyone who sees a stranded, entangled or distressed whale is urged to contact NPWS on 1300 072 757.

Experts believe the population of humpback whales are on the rise and that could lead to more encounters with fishermen.

"There's a lot more whales out there every year, The population is increasing by 10% to 11%." Ms Farrell said.

Story By | Joshua Becker, Breanna Holden & Simon Lauder