The California Department of Public Health announced late Friday that it would take steps to decertify the Porterville, Lanterman and Fairview Developmental Centers.
Health officials said they discovered "situations involving immediate jeopardy" to patients at the three facilities.
"The actions we're taking today are necessary to ensure that the Developmental Centers improve the quality of care at these facilities," said Dr. Ron Chapman, director of the health department.
The exact nature of the problems was unclear. Spokeswoman Anita Gore said documents providing more details would be posted on the department website after being redacted, but they were not online by late Saturday morning.
The facilities had been under review throughout the last year due to "deficient practices."
Phone and email messages left by The Associated Press on Saturday for representatives from the Department of Developmental Services, which oversees the institutions, were not immediately returned.
But the department said in a statement released to the Los Angeles Times that it has appealed against terminating the funding, that the centers "remain fully operational" and that it was "committed to making the necessary improvements that ensure appropriate and safe services at these facilities."
Health officials said they would work with the Department of Developmental Services to find a way to continue the Medicaid certification.
"We will work with them to try to ensure that they come into compliance so that they don't have to be terminated," Gore told the Los Angeles Times.
But if they fail to do so, they could begin losing some of their funding by mid-May, affecting the services received by 430 people.
However, Gore added, "We believe they will come back into compliance."
The moves by state officials come in the wake of a series of reports by the Center For Investigative reporting that found sloppy internal investigations of abuses at such centers, including the Porterville facility.