Canada has a few unaccompanied diplomatic posts, including Kabul and Tripoli.
The announcement comes as the federal government revealed a worrisome new development in the search for what is causing the symptoms that has affected 10 Canadians in all, diplomats and family members, including children.
The embassy will now be designated an unaccompanied post, meaning diplomats will have to live there alone.
There are now 15 staff in Havana, and Canada will review whether all the positions are needed, the official said.
Researchers found some of those affected heard a "novel localised sound at the onset of symptoms in their homes or hotel rooms", and many described it as "intensely loud, and with a pure and sustained tonality".
US diplomats in Cuba began reporting similar mystery symptoms in 2016 and Washington reportedly began investigating the possibility that they had been targeted by ultrasonic devices.More news: SUV that plunged into California river found, 2 bodies in it
Other possibilities include Jose Ramon Machado Ventura, the party's second secretary, who fought with guerrillas in the Sierra Maestro during the Cuban Revolution; and Ramiro Valdes, another former guerrilla who now serves as vice-president of the State Council and Council of Ministers.
The working theory is that whatever the cause, it happened in the housing, not the embassy, itself, because none of the Cuban staff who worked alongside Canadians suffered health problems.
Computer scientists at the University of MI said the problems may have been caused by eavesdropping devices and the ultrasonic distortion they produce, which can be harmful.
Canada has also received information from Canadian and American medical specialists that raised concerns of a possible type of acquired brain injury, the official said, while initial theories of a sonic attack first raised by USA officials previous year or mass psychosomatic causes are now considered to be improbable.
"The cause remains unknown, but could be human-made", Global Affairs said in a statement.
No tourists appear to have fallen ill and Canadian officials maintain Cuba is safe for holidaymakers.