Governor Pat Quinn said he disagrees with a Cook County judge who ruled the state must reinstate lawmakers' pay.
Quinn said he'll appeal and will seek a stay that would prevent any paychecks from being issued until the case is considered by a higher court.
However, Illinois Comptroller Judy Baar Topinka said she has instructed her staff to pay legislators.
Quinn halted legislators' pay during the summer because of their failure to reform Illinois' pension system.
Quinn's office said the stay was filed Thursday and the judge could take up the issue Friday morning.
Judge Neil Cohen ruled Thursday that Quinn's action is unconstitutional and that Topinka must pay lawmakers immediately.
Cohen said the state Constitution makes it clear lawmakers' pay can't be changed while they're serving their terms.