Mr Harper spoke about Maher Arar, a Canadian of Syrian origin, in a 15-minute telephone call with Mr Bush following a Canadian inquiry's report that cleared Mr Arar of any terror links.
"I indicated to President Bush that Foreign Minister Peter MacKay, would be sending a letter today to his counterpart, Secretary of State (Condoleezza) Rice, to launch a formal protest on the treatment of Maher Arar," Mr Harper told reporters.
"He had been unfairly deported where he had faced torture in Syria, and that American officials had not been candid and truthful in their dealings with Canadian officials in the case and had violated what we understand to be the protocols for such communications between our two governments," he said.
Mr Arar was stopped in New York, on his way to Canada from a trip to Tunisia, in September 2002 and was deported to Syria where he was jailed and tortured for more than a year.
"The president said that he would look at the complaint seriously, and we are expecting a response, an official response, to our complaint as well as assurances that we will not be facing that kind of conduct on the part of US authorities in the future, because we want to help the US in the fight against terrorism, and certainly, we share their concerns about security," Mr Harper said.
The inquiry headed by Judge Dennis O'Connor said in its report that US authorities had likely relied on faulty intelligence provided by the Royal Canadian Mounted Police (RCMP) to hold and deport the 36-year-old software engineer to Syria.
The mid-September report also urged Ottawa to register officially objections with Syria and the United States for their treatment of Mr Arar.