Mysterious Canadian-Iranian businessman Arian Azarbar made the startling allegations in an exclusive interview with QMI Agency.
Azarbar says he learned about the top secret operation during a relationship he had with Trina Kennedy, a senior national security investigator at Passport Canada.
"The Canadian government has said we had nothing to do with this, but it is a lie," Azarbar said. "The girl who was in charge of that file at Passport Canada, with whom I had a relationship, she told me about it."
"How come nobody is talking about that?" Azarbar added.
Azarbar said Kennedy confided details of the top secret identity switch after the couple enjoyed a night out and several drinks; he says Kennedy later asked him to forget what she had told him.
Azarbar has been accused in Montreal police documents of being a possible Iranian spy, allegations he has categorically denied.
Dubai police had no immediate comment on the claims.
Alexis Pavelich, a spokesman for Citizenship and Immigration Minister Chris Alexander (responsible for Passport Canada), did not answer any questions about Azarbar's allegations.
QMI Agency reported Friday that Alexander ordered an internal probe and Kennedy had been relieved of her duties after Azarbar made a series of allegations about her to federal authorities.
She's been locked out of all federal computers as well.
Azarbar provided a name and location in Canada where the alleged Mossad agent lived in Canada, but QMI Agency has decided to withhold that information to not endanger his personal safety and security.
QMI has been unable to reach Kennedy for comment.
In January 2010, Mahmoud al-Mabhouh, a military leader of Palestinian terror group Hamas, was suffocated by a team of killers at a Dubai hotel while he was on a unpublicized visit to the Emirates without bodyguards.
Al-Mabhouh was injected with a substance that left him paralyzed, authorities said.
Dubai police later said a 26-member hit team from the Mossad carried out the killing, entering Dubai on fake and forged passports under false names and they showed hours of hotel video surveillance footage of agents carrying out the killing and conducting surveillance.
Israel said there was no evidence to link the Mossad to the killing.