Judge Richard Leon of the U.S. District Court for the District of Columbia has been reviewing a consent decree reached by the government and the companies in October to allow their $69 billion merger. The deal has closed, although Judge Leon has required that some aspects of integration be halted during the review process.

Additionally, the Justice Department is required to respond to public comments on the consent agreement. It said in a court filing late on Tuesday that a lapse in funding as of midnight on Jan. 4 meant that the Antitrust Division could not process those comments until its appropriations were restored.

An exception could be made if the court orders them to do so, the department said in the filing.

The partial shutdown began hitting government agencies on Dec. 22 as part of a battle between the White House, which is demanding billions to build a wall on the U.S. border with Mexico, and congressional Democrats, who say the expenditure would be ineffective in slowing illegal immigration.

A spokesman for CVS had no immediate comment.

(Reporting by Diane Bartz; Editing by Susan Thomas)

By Diane Bartz