A statement from Canadian Public Safety Minister Ralph Goodale's office confirmed a British media report from Saturday, which said that Letts' UK passport had been torn up.
With his father being Canadian, Mr Letts has dual citizenship but Ottawa are said to be furious at the decision to revoke his British citizenship.
The United Kingdom is shirking its share of the worldwide community's duty to help keep the world safe from terrorism, the federal government suggested Sunday after the British Home Office revoked the citizenship of a dual citizen imprisoned in Syria.
Global law forbids people from being rendered stateless, but British law allows the United Kingdom to strip terror suspects overseas of their citizenship if they are a dual national or able to obtain citizenship of another country.
"Canada is disappointed that the United Kingdom has taken this unilateral action to off-load their responsibilities".
"Decisions on depriving a dual national of citizenship are based on substantial advice from officials, lawyers and the intelligence agencies and all available information", the spokesperson said.
"I think it's maybe Sajid that's a bit of a coward and in denial and naive, and obviously it's his last act [as home secretary] and he can move on and not have to even justify it", Mr Letts's father said.
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The elder Mr Letts and wife Sally Lane were convicted in June for funding terrorism after sending their son £223.
"This power is one way we can counter the terrorist threat posed by some of the most unsafe individuals and keep our country safe".
Despite expressing remorse over joining the terror group, Letts, 24, is now believed to have had his British citizenship revoked, sparking a diplomatic row with Canada.
Since his arrest, Letts told ITV news that he wished to return to Britain, but said that would be unlikely.
John Letts said previous year that Global Affairs Canada told the family for months that it was working to get their son released, but that the department eventually decided it was too unsafe.
Shamima Begum, who left Bethnal Green in London aged 15 to join Isis, was stripped of her British citizenship by Javid in February after it was argued she could apply to become a Bangladeshi citizen. I thought we had the right to innocent until proven guilty, the right of a trial, the right of free speech. Challenging the decision in the courts would require them to be in regular communication with their son, she added. "But I just want it to be... appropriate... not just haphazard, freestyle punishment in Syria", he said at the time. Global law prevents governments from making people 'stateless, ' so countries can only use the measure on those with two passports.
Bangladesh's foreign minister has said that Begum could be hanged for terrorism charges if she lands in Bangladesh.