The state budget passed last month gives Brown the authority to furlough workers to help close California's budget gap and save an estimated $402 million for the year.
Nineteen of the 21 state unions have reached contract agreements, but two, including the union that represents Caltrans engineers, are still negotiating. That union wants many private contracts eliminated, saying its engineers can do the job for less money.
Brown's order forces employees to take one day of unpaid leave a month, which amounts to a pay cut of about 5 percent.
The Associated Press contributed to this report.