USDA said that Foster Farms, owner of the three facilities, has until Thursday to tell the department how it will fix the problem. The company was notified Monday.
According to federal health officials, the salmonella outbreak linked to Foster Farms chicken is very complex and involves serious strains of the bacteria.
Sampling by USDA in September showed that raw chicken processed by those facilities included strains of salmonella that were linked to the outbreak. But the company has not recalled any of its products.
The Agriculture Department can halt production by withdrawing meat inspectors. In its letter to Foster Farms, USDA said the evidence suggests "the sanitary conditions in the establishment under which the product is produced could pose a serious ongoing threat to public health."
The agency had to close a system of labs called PulseNet that track illnesses. Those labs are now back open.
Two hundred seventy eight people in 18 states have been sickened by the outbreak -- most of them in California. The CDC says 42 percent have been hospitalized, about double the normal rate. Some of the strands were resistant to antibiotics, so some people could not be easily treated.
The USDA mark on suspect packages would read: P6137, P6137A and P7632. But until inspectors find the exact source of the contamination, the chicken is still being sold in stores.
Foster Farms said chicken is safe when fully cooked.
(The Associated Press contributed to this report)
