The companies, all located in northwestern Mexico close to the U.S. border, were shut down for failing to "comply with good agricultural and manufacturing practices," the department said in a news release issued over the weekend.
The department did not respond immediately Monday to interview requests.
Agricultural and health department specialists will visit the companies' growing areas and U.S. Food and Drug Administration officials will conduct inspections 15 days later, the department's release said.
"In addition to taking the relevant measures to address this case, the Mexican government is working to resolve long-term sanitation and product safety issues."
The Food and Drug Administration has identified eight brands of Mexican-grown green onions believed to have caused outbreaks of hepatitis A in Pennsylvania. Green onions also are suspected of causing outbreaks in Georgia and Tennessee. Three people have died and more than 600 fell ill in Pennsylvania, while more than 330 people became sick in Georgia and Tennessee.
The four companies closed down by Mexico's Agriculture Department are located near the border cities of Tijuana, Ensenada and Mexicali in the northwestern state of Baja California and the border city of San Luis Rio Colorado in Sonora state.
The Agriculture Department did not name the companies, but the FDA recently identified the companies that had been implicated in the shipment of contaminated onions as Dos M Sales de Mexico, located in Mexicali and San Luis Rio Colorado; Agricola La Laguna, a.k.a. Sun Fresh, of Ensenada; Tecnoagro International in San Luis Rio Colorado and Ensenada, and Agro Industrias Vigor in Tijuana, Ojos Negros and San Quintin, Baja California.
Hepatitis A is a virus that attacks the liver and can cause fever, nausea, diarrhea, jaundice, fatigue, abdominal pain and loss of appetite. Hepatitis A usually clears up on its own in about two months.