The Department of Personnel Administration filed the lawsuit Tuesday against Controller John Chiang in Sacramento County Superior Court.
The suit seeks a restraining order that would force Chiang to pay state employees $7.25 an hour, rather than their full salaries.
Last week, an appellate court ruled Schwarzenegger had the authority to order the minimum wage because the state has not passed a budget for the current fiscal year. His order would cover about 200,000 workers.
The controller said he doesn't have to follow the order because the state's computer payroll system can't handle the change. A telephone message left for the controller was not immediately returned.