Calgary police are in the early stages of what they say is a unique investigation into the in-custody death of a man being deported from Canada.

The 49-year-old man died following an altercation with two Canada Border Services Agency officers on a Tuesday afternoon flight to Amsterdam from Calgary.

"We can't tell you what nationality he is," said Staff-Sgt. Colin Chisholm of the homicide unit.

"We know he had been in Calgary for a significant period of time. We know he had been here for at least years."

Chisholm couldn't comment on why the man was being deported, but said he wasn't known to Calgary police.

Officers responded to the KLM Royal Dutch Airlines' plane that had returned to the gate after the altercation around 3 p.m.

Both the agency and police said the man was in medical distress and was taken to hospital, where he was pronounced dead around 4:30 p.m.

Police said an autopsy was completed Wednesday, but they are still trying to determine the exact cause and manner of death.

"The medical examiner's office is waiting for further testing to come back," said Chisholm. "The time frame is going to be months down the road before we can say the investigation is completed. We are going to await for the official autopsy to come back."

They said the man's name will not be released until his family is informed of his death.

"We are in the process of talking to the authorities in the (man's) home country to arrange next of kin to be notified," said Chisholm.

Police said the two border services officers were also taken to hospital, where they were treated for minor injuries and released.

Chisholm said he doesn't anticipate any charges based on what they know so far, but they are still speaking to witnesses to determine exactly what happened before the man went into medical distress.

"The airplane turned around and left," he said. "Obviously some of the witnesses were still on the flight so we didn't have firsthand opportunity to interview those witnesses right away. That creates a challenge for us."

Police asked anyone who witnessed the altercation to call, but they are also in contact with authorities in the Netherlands for help finding other people on board the plane.

"It's a traumatic event and people would be troubled by someone going into medical distress in front of them," said Chisholm.