SPRINGFIELD — About 30,000 state employees could be in line for pay hikes canceled more than a year ago by Gov. Pat Quinn.

Cook County Circuit Court Judge Richard Billik ruled Thursday that Quinn is obligated to pay raises worth 5.25 percent to members of the American Federation of State, County and Municipal Employees union.

The ruling marks the latest legal milestone in a years-long skirmish between the public sector union and the Democrat from Chicago.

At issue was Quinn’s 2011 decision to withhold negotiated wage increases provided in the union contract.

Billik ruled the state must pay what it can now and make employees whole eventually. Quinn must work with the state comptroller to place funds in a special trust that cannot be only be used to pay employees what they are owed.

“This ruling is a strong affirmation of the union’s clear and simple position: Employees must be paid the wages they are owed, and a contract cannot be unilaterally discarded,” AFSCME Council 31 executive director Henry Bayer said Friday.

The governor’s budget office plans to appeal.

Employees affected by the decision include those working for Corrections, Human Services, Juvenile Justice, Natural Resources and Public Health.

The contract called for AFSCME workers to receive a 4 percent raise on July 1, 2011. The union agreed to defer half of that increase to save the state money during tight budget times.

Quinn then canceled a separate 1.25 percent raise due on Jan. 1, 2012 and never paid the previously agreed to increases, citing a lack of state funds.

For a state worker earning $50,000 annually, the increase could amount to about $2,000.

The legal fight over the pay raises is just one of a handful of battles being waged between AFSCME and Quinn.

A separate union lawsuit has stopped the governor from closing prisons and prison facilities in Tamms, Dwight, Carbondale, Murphysboro and Decatur.

The governor last month terminated AFSCME’s contract while the two sides negotiate a new contract. Negotiators have failed to reach an agreement after nearly a year of bargaining.

Bayer urged the governor to drop the ongoing legal battle.

“Governor Quinn has wasted hundreds of thousands of taxpayer dollars with the goal of preventing middle-class public employees from being paid according to their contract and the law,” Bayer said.