The Maher Arar inquiry was told on Thursday that the RCMP shared intelligence with Syrian officials in the fall of 2002.
RCMP Supt. Mike Cabana who headed up the investigation in the Ottawa area said Canadian officials were concerned Arar was being abused early in his captivity in Syria, but they exchanged intelligence anyway.
"As appalling as it may sound to you, part of our duties in Canada, in trying to protect the Canadian public, means that from time to time we have to deal with countries that don't necessarily have the same record as we do. And don't necessarily treat their prisoners the same as we do.
"And I would submit to you that if we didn't consider dealing with these countries, the security of Canadians would be greatly at risk," he told the inquiry.
Cabana says intelligence officers discussed the matter just a few weeks after Arar was deported to Syria by the United States.
Canadian diplomats had met with Arar in Syria and sent a report back to Canada.
Cabana says everyone knew there was a risk Arar was being poorly treated.
On Wednesday, Cabana told the inquiry Canadian intelligence was being shared with foreign countries, including the U.S. and Syria.
Cabana said in the wake of the Sept. 11 attacks in 2001, his superiors told him to waive some of the normal safeguards on the transfer of sensitive information.
Arar, a Syrian-born Canadian citizen, was deported in September 2002 by U.S. authorities after they arrested him in New York as he was flying home to Canada.
The Ottawa engineer spent almost a year in prison in Syria and says he was repeatedly tortured.
Also on Thursday, Arar stormed out of the inquiry looking into his detention and alleged torture, apparently frustrated over repeated objections from government lawyers.
The lawyers objected to much of the testimony at the inquiry on the grounds that it is a matter of national security.
After a short period Arar returned to his seat.