The children, 13-year-old Lindsey Brillant-Marcoux and his 11-year-old sister Karen, had fatal levels of carbon monoxide in their systems and showed signs of smoke inhalation, the coroner found.
An autopsy on their father, Jocelyn Marcoux, 47, showed the same findings
While the coroner's report does not explicitly state he is to blame for their deaths, it describes the events leading up to the fatal fire and says that Marcoux is the only one who could have brought the children to the garage, located on the family's property about 140 kilometres southwest of Quebec City.
It also states an adult set the fire.
The three bodies were discovered in the detached garage early on the morning of July 10, 2012.
The badly burned remains, found close together in the metal building, were identified through dental records.
The children's tattered pajamas were still identifiable when the coroner arrived on the scene.
Marcoux's family described him as a man who loved his children, who took care of them and never showed any signs of violence toward them.
However, a brewing custody battle with the children's mother, who had separated from Marcoux a decade earlier, was causing him a significant amount of anxiety, according to the coroner's report.
Marcoux had sole custody of the children, but their mother was asking the courts for that arrangement to be amended. The court was to hear that request on the day the children died.
Marcoux's friends and family said he was worried about losing custody of the kids and that they might have to change schools. They told investigators there was no sign he might harm the children or himself.
His ex-partner said he had never shown any sign of psychological problems in the past or substance abuse.
Marcoux's neighbour, thought to be the last person to have seen the children alive, said that sometime after midnight on July 10, he heard a noise behind the home where Marcoux lived with the children.
It wasn't unusual to see people outside at that hour as families often slept in trailers on the property during the summertime, he told investigators.
There had been some recent thefts in the area, so the neighbour stuck his head out the window to make sure everything was all right.
He said he saw Marcoux, Karen and Lindsey from the back of the house. He called out to Marcoux to explain that he wasn't trying to spy on them and the neighbour replied that there was no problem.
The three continued on in the direction of the garage, the corner's report states.
The neighbour then said he was woken up by the sounds of his dogs barking. He saw a glimmer of an orange glow from the window and then saw his neighbour's garage in flames.
Investigators found gas and intact propane tanks in the area of the garage. The three bodies were found close together near the back of the structure, the girl's head resting on her father's legs.
The coroner's report concludes that Marcoux's death was intentional and self-inflicted.
The reports on the children end with one line: "The deaths were of a violent nature."