The commission may seek fines later, the report said.
It also seeks fines of up to $25,000 per violation per day.
The Justice Department said it had not sought fines or criminal charges.
It can also seek heavy fines on landlords who discriminate.
The suit seeks an injunction and fines of $25,000 a day for the two years the Government says the company was in violation.
The school board agreed not to seek fines against union leaders and members if teachers returned to work.
That meant filing a civil case, and seeking fines.
Federal officials have not decided whether to file a civil suit and seek fines.
The complaints seek fines of up to $30,000 per driver.
During negotiations in 1999 and 2002, the city sought crippling fines on any transit workers who walked out.