Mexican authorities say the 35-year-old was on a small inflatable vessel as it was returning from a snorkelling tour Wednesday off the coast of Cabo San Lucas.
Capt. Vicente Martinez with the Mexican navy identified the victim as Jennifer Karren.
On Thursday, WorleyParsons, the project and consulting company in Calgary where Karren worked for six years, offered their condolences to her family and friends.
“Jen died in a tragic accident while holidaying in Mexico," said a statement from the company, which said she was a member of their mail services and facilities management team.
"Her colleagues remember her as a positive, friendly teammate who was willing to help out whenever she could. She always spoke kindly of everyone with whom she came in contact.
The company said they are offering support to those deeply affected by the death.
The Department of Foreign Affairs has also provided a statement saying their thoughts were with "the family and friends of a Canadian citizen who passed away in Mexico. Canadian consular officials in Cabo San Lucas are providing consular assistance to the family in this difficult time.”
The tour company that owns the boat, Cabo Adventures, said the whale suddenly appeared and the captain tried to avoid it. The animal hit the side of the boat, injuring two passengers and tossing the Canadian overboard.
"The boat returned immediately to where the guest was in the water," Felipe Diez-Canedo, executive director of the tour company, said in an email.
A guide and another passenger jumped in to save the woman, he said. Another passenger who is a nurse tried to revive her.
A navy rescue team arrived and provided medical care until they were met by paramedics on shore. Karren was pronounced dead at a private hospital.
Martinez said her husband had been with her and told officials she lost consciousness after the whale hit the boat.
Sergio Villarreal with the Baja California Sur state prosecutor's office said she died from head trauma. He said he had never heard of such a death before.
The Attorney General's Office for Environmental Protection released photos of the life-saving efforts on the open tour boat.
They show the craft is about 7 1/2 metres long and has twin outboard motors. It appears undamaged in the photos.
The tour company said one of the two injured passengers was released from hospital and the other was returning to the United States for further treatment, although not for a life-threatening injury.
Collisions between whales and boats are not totally unknown in Mexico, where whales come to breed in coastal lagoons in winter. Authorities generally require boats to stay a safe distance from the marine mammals in whale-watching areas and protected reserves, but those rules don't apply in the area around Cabo San Lucas.
In January 2014, a U.S. tourist and three others were injured when a boat and a humpback whale collided off the coast of Baja California.
Jorge Urban, a professor of biology at the Baja California State University, said in his 30 years of studying whales he has never "heard of an accident like this ... in which passengers are pitched into the sea and one dies."
While officials identified the animal that struck the boat as a grey whale, Urban said it was almost certainly a humpback.
Anna Hall, a marine mammal zoologist in Victoria said all whales need to surface to breathe, but both grey and humpback whales also like to jump. Because it's the end of their breeding season, males tend to breach more to demonstrate their strength to potential mates.
Hall suggested the whale is likely to have been unaware of the boat.
"Of all the things a captain and a crew need to worry about in the daily operations of vessel movements on the water, no matter where you are, having a whale breach and land on you is way down the list," she said.
"It's a very rare event."
— By Chris Purdy in Edmonton and Alexander Panetta in Washington, with files from Associated Press, CFFR