The employees, with the city's General Services Department, were in the fire department's storage area and truck repair shop when the incident occurred, according to the Detroit Metro Times.
One person was hospitalized with injuries to his leg and scrotum. The extent of the second person's injuries was not immediately clear.
Deputy Fire Commissioner Dave Fornell described the situation to the Times as a "prank" that ended badly, while Mike Nevin, president of the Detroit Fire Fighters Association said, "This is an absolute embarrassment."
City officials on Wednesday didn't know who placed the firecrackers underneath the toilets. Nevin cleared his association members of any wrongdoing.
The Detroit Police Department — which is said to be investigating — did not immediately return Fox News' request for comment.