The order will affect about 40 percent of the more than 8,200 inmates at the two prisons, said Joyce Hayhoe, a spokeswoman for the receiver's office.
"The state of California has known since 2006 that segments of the inmate population were at a greater risk for contracting Valley fever, and mitigation efforts undertaken by CDCR to date have proven ineffective," she said in an emailed statement. "As a result, the receiver has decided that immediate steps are necessary to prevent further loss of life."
That creates problems for the corrections department, which faces a December deadline to reduce overcrowding in prisons statewide by an additional 9,000 inmates as part of a federal court order to improve medical and mental health care.
The department had been focused on trying to minimize the spread of the dust that carries the spores that cause Valley fever.
"If there are ways to reduce or prevent Valley fever, period, regardless of who the inmates are, that would probably be the best thing all around," Callison said.
Steps include controlling dust measures during construction, giving surgical masks to inmates and employees who request them, and providing education materials to employees and inmates. The corrections department is installing air filters and is considering measures to cover up dusty areas and screen out more dust from entering prison buildings.
Valley fever is found most often in the southwestern United States, with about a quarter of the cases in California and more than 70 percent in Arizona, according to the Centers for Disease Control and Prevention. The number of cases has risen over the years and topped 20,000 in 2011, the CDC reported in December.
John Galgiani, a professor of medicine at the University of Arizona. said the situation at the Pleasant Valley and Avenal prisons is a "public health emergency."