The front of the red double-decker bus was sheared off and the engine of the VIA Rail train had derailed, but the train cars remained upright with little noticeable damage.
"Paramedics had to declare five persons deceased on scene, nothing could be done. And of the 31 that were transported, we've just been advised that one was deceased in hospital, for a total of six deaths at this point," Anthony DiMonte, chief of Ottawa Paramedic Services, told a news conference.
He said 11 of the people taken to hospital had been in critical condition.
Ambulances and fire trucks swarmed the scene in the rural west end of Canada's capital city as emergency workers helped train passengers disembark past the wreckage of the bus. Five bodies appeared to be wrapped in yellow tarps beside the train track. One had a purse and a backpack next to it.
One passenger on the bus said the driver did not seem to notice the oncoming train or that the track-level signals were flashing. He said some passengers tried to warn the driver before the collision.
"From what I can tell the bus driver did not notice that these train-tracks signal lights were on and the gates were down. People screamed on the bus shortly before the crash because he was not stopping," Gregory Mech, a passenger on the top level of the double-decker bus, told CBC Television.
"I could see that there were bodies on the train tracks. It was horrible. There's just no other way to explain it. Some people were upset and crying."
Ottawa emergency officials said the collision occurred at 8:48 am EDT (1818 IST). VIA Rail, which operates national rail passenger service in Canada, said there were no major injuries reported on the train.
Passengers on the train, which was heading to Toronto, said they felt a small impact.
"All I felt was a bump, and I saw a bit of smoke. I thought we were going off the track ... I was afraid we were going to flip over," passenger Robert Gencarelli told reporters on the scene.
He said he was startled when he got off the train and saw how badly the bus was damaged.
"That hit home."
Another train passenger, who did not give his name, said he saw the bus rolling toward the train tracks and knew the collision was about to happen.
"I saw it before it happened. I was expecting something. There was a big bang. ... The bus was rolling. It didn't stop."
The crash occurred at a level crossing surrounded by corn fields.
A reunification center was set up for families and friends looking for passengers on the bus and train, the City of Ottawa said.
Canadian Prime Minister Stephen Harper said he was "deeply saddened" to hear about the collision, which came just months after a runaway freight train crash and explosion killed 50 people in Lac-Megantic, Quebec.
"Our thoughts and prayers are (with) the families of those involved," Harper said on Twitter.
Canada's two big railroads - Canadian National Railway and Canadian Pacific Railway Limited - are reviewing safety standards after the July 6 Lac-Megantic crash that destroyed the center of the small Quebec town.