Metro filed a lawsuit against Local 2 — one of its smaller unions, claiming that it should not have to give clerical and administrative workers higher wages.

The suit comes after Metro was court-ordered to pay higher wages retroactively to its largest union, Local 689.

The Local 2 lawsuit was first reported by the Examiner.

Metro and Local 2, which represents mostly clerical-type jobs for 709 transit agency workers, had a contract that expired June 30, 2008. But the parties hit an impasse over “wages, pensions, health care benefits, subcontracting and other issues,” according to the lawsuit.

They went to an arbitration, which awarded pay increases of 2 percent to 3 percent each year from 2008 to 2011.

In the lawsuit, Metro called the arbitrator’s actions “arbitrary and capricious and clearly exceeded its authority.”

Metro also disagrees with the arbitration board’s view of subcontracting for clerical type jobs.

Dan Stessel, Metro’s chief spokesman, said in a statement that the agency regrets “that this creates uncertainty for our employees, however we are appealing because the Arbitration Board’s award would interfere with our ability to supplement our workforce using contractors.”

That could cause a “slow down,” he said, “of much-needed safety and state of good repair improvements.”

He said the arbitration board also failed to consider “the financial challenges that Metro currently faces.”

Metro is facing a $116 million budget shortfall in fiscal 2013 and has proposed asking riders to pay higher fares and local jurisdictions to pony up more money in their subsidies.

Follow me on Twitter @postmetrogirl.