State workers were furloughed 46 days when the governor issued a similar order in February 2009 which resulted in a pay cut of about 14 percent for workers.
It is unknown how long this new round of furloughs will last. Schwarzenegger and lawmakers are entering the fifth week of the new fiscal year without a balanced budget.
"Without a budget in place that addresses our $19 billion budget deficit, every day of delay brings California closer to a fiscal meltdown," Schwarzenegger said in a statement.
State Controller John Chiang has warned in the past that he will start issuing IOUs in August or September if the budget stalemate drags on in the Legislature.
Wednesday's new order exempts those who work for departments that collect revenue, including the Franchise Tax Board. Also exempt are about 37,000 workers in six unions that reached tentative labor agreements with the Schwarzenegger administration.
The furlough puts pressure on other unions that have not agreed to the governor's demands for pension reforms. Unions have also been fighting the governor's efforts to impose the federal minimum wage while the state operates without a budget.
"To once again force state employees to take unpaid furloughs is just another punitive measure by Governor Schwarzenegger because he couldn't impose minimum wage," said Patty Velez, president of the California Association of Professional Scientists, which represents 11,000 state employees.
AP contributed to this report.