A man has died after his boat was struck by a whale and flipped in Sydney waters.

Two men were flung from their vessel off Cape Banks at La Perouse in Botany Bay about 6am on Saturday.

Water police responded after receiving reports a whale may have breached near or onto the boat, NSW Police said.

One man was pulled from the water unconscious.

“Attempts to revive him were unsuccessful and he was declared deceased,” police said in a statement.

A second man was treated by paramedics before being taken to hospital in a stable condition.

‘There are lots of whales out there’

Acting Superintendent Siobhan Munro said with more whales about than usual the incident was tragic but not unexpected.

“Right now there are lots of whales out there (so) it’s not unheard of,” she told reporters in Sydney.

“Early reports are that a whale may have breached near the boat or onto the boat.”

Ms Munro said a witness onboard a vessel nearby called emergency services after seeing a boat “doing laps without anybody on board”.

“The skipper stayed as close as he could to the deceased and was doing all he could to keep him afloat until police arrived,” she said.

NSW Police Minister Yasmin Catley said the incident serves as a stark reminder of how dangerous it can be out on the water.

“Whoever would have thought that that would have occurred. So it’s terribly tragic,” she said.

“Two guys would have got up to go out and enjoy themselves fishing … something that most people in NSW love to do, and we’ve ended up in a tragic set of circumstances.”

The vessel will undergo forensic examination and the Foreshore Road Boat Ramp at Botany has been closed as inquiries continue.

The Australian Maritime Safety Authority (AMSA) said there are an incredible amount of whales around this year and advised swimmers and boaters to stay 100 metres away from a whale and 300 metres from a whale with a calf.

The death comes on the first day of National Safe Boating Week.

AMSA acting manager of vessel operations Shontelle Chamtaprieo said safe boating practices can make the difference between life and death on the water.

​”Life jackets and distress beacons significantly increase the chances of survival in boating incidents,” she said.

-AAP