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."
The Department of Developmental Services, which oversees the institutions, has appealed termination of the funding.
The department said in a statement released to The Associated Press that the centers "remain fully operational" and it is "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.