The Illinois Supreme Court on Friday declined to take up the question of whether state employees can be paid in full during the ongoing budget impasse, setting the stage for what could be a lengthy legal battle as Republican Comptroller Leslie Munger continues sending out paychecks.

The decision dealt a blow to Democratic Attorney General Lisa Madigan, who had asked the court to intervene after judges in Chicago and downstate delivered contradictory rulings on the issue last week.

By declining Madigan’s emergency motion, the high court effectively said that the matter will need to move through the lower courts first, and there are two cases in which that could happen.

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One was filed in St. Clair County, where a judge ruled last week that failing to deliver paychecks would violate state workers’ collective bargaining agreements. Madigan is appealing that decision, but Munger has used it to justify sending out full paychecks to state workers.

The other case was filed in Cook County, where a judge last week told Munger to pay only the $7.25-per-hour federal minimum wage until state government gets a budget in place. Munger argued that her office did not have the technical ability to make the payroll change. On Friday, an appeals court voided the ruling and sent the case back to the Cook County judge to consider “hardships” to Munger and taxpayers.

Munger said the appellate court’s ruling “removes any conflict between court decisions and allows my office to continue paying all state employees for their work.”

At any rate, the state Supreme Court’s Friday decision not to immediately take up the two cases relieves pressure on Republican Gov. Bruce Rauner, who has tried to minimize fallout from his feud with ruling Democrats in the General Assembly by making sure paychecks keep flowing to workers.

Rauner and Democrats disagree over the new governor’s pro-business, anti-union agenda, which has stalled a deal on a budget for the financial year that began July 1.

The Associated Press contributed.