An outside agency is investigating an allegation that a sexual harassment complaint against Brooks was ignored by the city's office of compliance. He is accused of coming on to a female auditor who works at the Chicago Fire Department and threatening her job when she refused the advances.
Brooks has been on vacation since March.
Mayor Daley's spokeswoman Jackie Heard said the sexual harassment investigation will continue and the outcome could affect Brooks' pension.
Brooks joined the Chicago Fire Department in January of 1980 and moved up in the ranks. In 2008 he was confirmed as the city's second African-American fire commissioner.