
Canada's foreign affairs department said in a statement it "can confirm that five Canadian citizens were involved in the bus hostage taking in Manila. Among these, we are aware that three have died."
Canadian consular officials in Manila have offered assistance to those involved and their families, the department added.
Hong Kong has said they were dual nationals living in Hong Kong.
According to public broadcaster CBC, two young girls, Song Yi (Jessie) Leung and her sister Chung See, and their father Kam Wing (Ken) Leung were slain during the hijacking.
The girls' brother, Jason Leung, 18, was hospitalized with a skull fracture. His mother is reportedly at his bedside.
On Monday, a disgruntled former police officer hijacked a tourist bus in downtown Manila, which the Hong Kong government said had been carrying 21 Hong Kong tourists.
A 12-hour standoff that ended when police fired tear gas into the bus and a sniper shot the gunman in the head. But by then eight of the tourists on board had been killed, sparking a torrent of criticism over the police tactics.
Canadian Foreign Minister Lawrence Cannon said: "Canada welcomes the commitment of Philippine authorities to conduct a full investigation of the incident."