RALEIGH — North Carolina officials have increased their estimate of the number of people with mental illness who may have to leave adult care homes because of a conflict with the federal government over how the state pays for their care.

State officials said this week the number of facilities whose patients may have to leave has increased from 38 to 52, potentially putting more than 1,200 residents out of the facilities where they are now living.

“We’re working on this constantly,” said Lanier Cansler, secretary of the N.C. Department Health and Human Services. “The problem is there’s no easy solution.”

DHHS spokeswoman Renee McCoy also said this week that the state had missed a Sept. 1 deadline to provide a plan to federal regulators.

But Cansler clarified Wednesday that his spokeswoman was incorrect. There had never been a hard deadline to have the work done, he said.

“Originally, the feds had suggested that we try to do the assessments on these facilities by September,” Cansler said. “We haven’t missed any deadlines. The question was how soon could we get the assessments. We’re preparing to start the assessments soon, over the next couple months.”

The federal agency that oversees Medicaid notified the state earlier this year that it was in violation for using the medical program to pay for the care of people with mental illness housed in dozens of adult care homes scattered across the state.

Medicaid rules forbid payment for care in facilities where more than half of the residents have a primary diagnosis of mental illness.

Medicaid officials could respond by ordering the state to stop payment to adult care homes termed as institutes of mental disease.

No one seems sure of where these people might go if they are forced out of the homes. Advocates for people with mental illness say they are concerned many of the affected residents will end up in emergency rooms, jails, homeless shelters or on the street.

Lee Millman, a spokesman for the federal Centers for Medicare & Medicaid Services, said this week she could not immediately comment on the situation in North Carolina.

The Medicaid issue with adult care homes is one of three simultaneous challenges now facing North Carolina’s troubled mental health system, which has lurched from one crisis to the next since the state attempted an ambitious but flawed reform plan 10 years ago.

As part of that reform, the state eliminated about half of its beds in government-run psychiatric hospitals, closing the doors of such long-serving facilities as Dorothea Dix Hospital in Raleigh. The result has been long waiting lists for beds, with people in the midst of a psychiatric crisis often languishing for days, even weeks, in the emergency rooms of community hospitals ill-equipped to care for them.

In July, the U.S. Department of Justice issued findings that the state’s reliance on using adult care homes to house people with mental illness violates the Americans With Disabilities Act.

As the state tries to negotiate a settlement with the Justice Department, it must also find a solution palatable to federal Medicaid officials to meet the needs of people with disabilities eligible to receive government support for in-home assistance. Medicaid funding for those services is set to end in February.

Cansler has termed the trio of issues a “perfect storm” that could cost the cash-strapped state government more than $100 million to fix.

In an Aug. 10 letter to U.S. Health and Human Services Secretary Kathleen Sebelius, Cansler warned the situation could “likely lead to a tremendous destabilization and potential collapse of the entire (adult care home) industry in North Carolina.”

“Such a collapse would leave thousands of North Carolina’s aged and disabled residents without access to critical housing and care if necessary transitions are not properly planned and successfully implemented,” Cansler wrote, pleading with Sebelius to give the state more time to come up with a plan.

Cansler said Wednesday he has not yet heard back as to whether his request for more time had been approved.

Cansler’s analogy to an unforeseeable weather disaster frustrates advocates for people with disabilities, who say the current situation is the very predictable result of a decade of mismanagement and underfunding by the state.

“The state’s failure to provide appropriate community based services to people with mental illness is long standing and part of failed mental health reform,” said Vicki Smith, the executive director of Disability Rights North Carolina. The group filed the 2010 ADA complaint with the Justice Department that triggered the federal finding that the state is in violation.

“The state should develop an array of services and housing options so that treatment and living options are matched to the specific needs and preferences of the individuals,” Smith said.