The request follows a USA Today investigation that identified dozens of people imprisoned in North Carolina for what a federal appeals court later determined were not federal crimes, USA Today reported Wednesday.
ACLU lawyers said up to 3,000 inmates and probationers could be eligible to be freed or have their sentences reduced.
Although Justice Department lawyers have conceded the prisoners are "legally innocent," the department has made little effort to notify them and has argued in court to keep them locked up, the ACLU said.
"Instead of taking proactive steps to ensure that the innocent are freed, it has thrown up roadblocks," the ACLU said.
The complicated cases involve federal gun possession laws and North Carolina's method of classifying felons and sentencing them.