STOCKTON (CBS / AP) — The head of California’s prison system said Tuesday a court order to evacuate thousands of inmates from two Central Valley lockups hit hard by an infectious disease could lead to racial conflicts elsewhere.

Corrections Secretary Jeffrey Beard said officials had been awaiting the results of a U.S. Centers for Disease Control study on the outbreak before deciding how to respond.

U.S. District Judge Thelton Henderson on Monday criticized Gov. Jerry Brown’s administration for delaying significant response to the problem for years and for its recent proposal to delay action for several months until the CDC can complete health studies at the prisons.

The judge ordered as many as 3,250 inmates evacuated within 90 days, but he left it up to corrections officials to determine where they should go.

The two prisons are about 10 miles apart and 175 miles southeast of San Francisco. Evacuees will include most of their black, Filipino and medically at-risk inmates because they are considered the most vulnerable to health problems from the fungus, commonly called valley fever.

Beard told The Associated Press that moving those inmates to other prisons could upset carefully set racial balances and exacerbate gang violence.

“We have to be very careful so we don’t destabilize other institutions and create other problems while we’re trying to solve this problem,” said Beard, who also is grappling with a separate court order to ease overcrowding of the entire prison system.

“So you know it really is making things very complex and difficult, and of course my concern is it could eventually cause some adverse effect in some other institution, some unintended effect, and we certainly don’t want to see that happen,” Beard said.

Beard said government lawyers are reviewing the judge’s order, and no decision on an appeal has been made.

The judge on Monday gave the state seven days to begin moving the inmates from the two prisons.

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