Florida health care agencies have acted with "deliberate indifference to the suffering" of frail and disabled children by offering parents no "meaningful" choice but to warehouse their children in nursing homes along with elders, the U.S. Department of Justice said in a lawsuit against the state filed Monday.

The Justice Department's civil rights division accused the state of violating the landmark 1990 Americans with Disabilities Act — which forbids discrimination against people with special needs — by funding and managing its community programs so poorly that hundreds of children have been forced to live, and sometimes grow up, in institutions for the elderly.

Last September, the Justice Department told state health administrators that Florida's system of care for frail and disabled children was discriminatory, because it failed to offer parents meaningful opportunities to care for their medically fragile children outside large, segregated institutions. While the state made half-hearted reforms, the DOJ said, the discrimination persisted.

The Justice Department, the lawsuit says, "has determined that compliance with the ADA cannot be secured by voluntary means" by the state. The DOJ is asking a federal judge to declare the state's program for disabled children in violation of federal law and to force the state to cease warehousing children in institutions.

"Unnecessary institutionalization denies children the full opportunity to develop and maintain bond with family and friends; impairs their ability to interact with peers without disabilities; and prevents them from experiencing many of the social and recreational activities to contribute to child development," the lawsuit says.

It adds: "Many of the institutionalized children remain in facilities for very long periods of time, even when it is apparent that their medical conditions would permit return to the community with appropriate supports."

The lawsuit, aimed primarily at the state's Agency for Health Care Administration, the Department of Health and the Department of Children & Families, follows several months of in-depth reporting on the children's plight by the Miami Herald.

A spokesman for the Agency for Health Care Administration said the federal government is meddling in state business.

The suit appears to be one of the final official acts of Thomas E. Perez, who headed the DOJ's civil rights division until gaining Senate approval last week to be President Barack Obama's labor secretary, an appointment that was held up for months.

To a large degree, the controversy is over money: Even as Florida health administrators have increased the payment for pediatric nursing-home beds by close to 30 percent — the state will now pay about $550 per day for a child in a nursing home — the state has relentlessly cut services for families struggling to care for a severely disabled child at home.

Reimbursement rates for service providers in the community have remained stagnant since 1987, the suit says, resulting "in shortages of nursing services in certain parts of the state."

And three years ago, state lawmakers simply cut $6 million from a program that pays for private-duty nursing care for Floridians who wish to remain outside institutions.

One program that is designed to allow parents to care for disabled children at home or in community settings now has a wait list with about 22,000 names. As of last fall, the lawsuit says, more than half of the Floridians have been waiting for care for five years or longer. Additional dollars for the program set aside by lawmakers earlier this year will only help "fewer than five percent" of those waiting.

As money for community care dwindled — and payments to nursing homes dramatically increased — the number of children living in institutions also grew, the lawsuit says. In 2011, the Agency for Health Care Administration, acting at the behest of a large Broward nursing home, withdrew its own provision limiting the number of children in each nursing home to 60. Close to 200 children remain in nursing home beds in the state.

"As a result of the state's actions and inaction, the state has forced some families to face the cruel choice of fearing for their child's life at home or placing their child in a nursing facility," the DOJ said in a press release.

In a short press release, the state Agency for Health Care Administration, AHCA, criticized the federal government, saying it is meddling in Florida's affairs.

"Today's Obama Administration action shows that Washington is not interested in helping families improve, but is instead is determined to file disruptive lawsuits with the goal of taking over control and operation of Florida's Medicaid and disability programs," AHCA Secretary Liz Dudek said. "Florida has made many improvements in its already strong program of caring for medically complex children and helping their families cope with their everyday challenges."

Since the controversy began, the state has moved 31 children from nursing homes back into the community, has sent six other fragile children directly from the hospital back to their families, and another three children in the custody of the state were discharged to a medical foster home, where they receive care in a home-like setting, Dudek added.

But a Miami civil rights lawyer who has also sued the state over the institutionalization of children called Dudek's actions mere "window dressing."

"This is an indictment of the state of Florida with regards to how they treat children with disabilities," said Matthew Dietz, whose suit is pending. "It means the U.S. government takes very seriously that nursing homes are not an appropriate place to put children with disabilities."

"The suit I think will show to both the nursing home industry and to states that it is not a viable option to place a human being who could feel, who could see, who could interact into a geriatric nursing home where they have no connection with their family, with their communities," Dietz said. "It's an inhumane practice."

The Justice Department began criticizing the state's practice of segregating disabled children last September, when it sent Florida a 22-page letter claiming that it was violating the Americans with Disabilities Act by placing frail children in nursing homes for the elderly. The letter, based on a six-month investigation, said that more than 220 children had ended up in geriatric nursing homes because of state funding cuts for in-home nursing care and other services.

Late last year the Justice Department issued a confidential "settlement proposal," which the Herald obtained, that demanded Florida stop funneling children to geriatric nursing homes, stop cutting in-home nursing care for disabled children and consult with children's primary doctors before cutting services for them.

Florida's practice of housing hundreds of severely disabled children in geriatric nursing homes has faced intense scrutiny after two children died in a Miami Gardens nursing home. Golden Glades Nursing & Rehabilitation Center, formerly called the Florida Club Care Center, faced fines of more than $300,000 in connection with the death of Marie Freyre, a severely disabled 14-year old. Freyre died in April 2011 after child welfare administrators sent her 250 miles from her Tampa home to Golden Glades against her mother's emphatic wishes. The child died within 12 hours. Golden Glades shut down its pediatric wing earlier this year.

Bryan Louzada died in the same facility in July 2010, a year after his mother was forced to deposit him there when state health administrators repeatedly refused to pay enough for in-home nursing care.

Another nursing home, Lakeshore Villas in Tampa, also is shutting its doors after the federal Medicaid and Medicare programs announced they would no longer reimburse for care in that facility.

A total of five children have died in Florida nursing homes during the last half of 2010 — and 130 have died since January 2006, according to state records. Medically fragile children who live with parents or in a community setting die in far lower numbers, records show.