Toronto EMS said the man was taken to St. Michael's Hospital with a gunshot wound.
The shooting happened at approximately 8 p.m.
Toronto police said the Ontario Special Investigations Unit (SIU) has invoked its mandate.
The SIU is called in whenever police officers are involved in incidents in which someone has been seriously injured, dies or alleges sexual assault.
Subway service has been halted between Union and Bloor stations.