It has affected diplomatic staff and their families in Cuba.
Canada is still investigating the cause of the symptoms that were first reported by Canadians connected to the Havana embassy in 2017 and have also affected U.S. diplomats in Cuba.
The embassy will now be designated an unaccompanied post, meaning diplomats will have to live there alone.
Canadian officials will also review the 15 roles at the embassy to see whether some staff can be brought home.
An official told reporters that the Canadians affected have suffered concussion-like symptoms that include dizziness, nausea, headaches and trouble concentrating.
The United States said in March it was making permanent last year's decision to slash staffing at its Havana embassy by around two-thirds as the alleged health incidents among its diplomats remained unsolved.
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.
Canadian officials said there had been no new instances since 2017 but families who had returned to Canada had continued to suffer symptoms, sometimes improving before their illness returned again.
The mysterious illnesses were originally believed to be caused by covert sonic attacks.
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. "Additional research is needed to better understand this", said a statement issued by the ministry on Monday.
"The cause remains unknown, but could be human-made", Global Affairs said in a statement.
More than million Canadian tourists visit Cuba every year.
Cuba has repeatedly denied either involvement in or knowledge of any attacks and has said its own investigation into the illnesses has turned up no evidence of deliberate action.