WASHINGTON — When patients in South Dakota seek help for serious but manageable disabilities such as severe diabetes, blindness or mental illness, the answer is often the same: With few alternatives available, they end up in nursing homes or long-term care facilities, whether they need such care or not.

In a scathing rebuke of the state’s health care system, the Justice Department said on Monday that thousands of patients were being held unnecessarily in sterile, highly restrictive group homes. That is discrimination, it said, making South Dakota the latest target of a federal effort to protect the civil rights of people with disabilities and mental illnesses, outlined in a Supreme Court decision 17 years ago.

The Obama administration has opened more than 50 such investigations and reached settlements with eight states. One investigation, into Florida’s treatment of children with disabilities, ended in a lawsuit over policies that placed those children in nursing homes. With its report Monday, the Justice Department signaled that it might also sue South Dakota.

While the administration has received widespread attention for investigating police abuses and supporting the rights of gay and transgender people, the Justice Department has also steadily made these cases part of its civil rights agenda. The government says that those efforts have allowed more than 53,000 Americans with disabilities to leave institutions or avoid them altogether. It is a small number compared with the 250,000 working-age people who are estimated to be needlessly living in nursing homes, but advocates say the federal campaign has had significant effects.