U.S. District Judge William Young in Boston was randomly assigned the case despite the Justice Department's contention that the lawsuit should be heard by another judge who is overseeing a separate antitrust case involving JetBlue.
The Justice Department on Tuesday argued that Sorokin should hear the Spirit case as well because both involved "an assessment of JetBlue's network plans, aircraft orders and configurations, and pricing strategy."
Sorokin, an appointee of Democratic former President Barack Obama, on Wednesday in a brief order said the Spirit case was wrongly assigned to him because it was "incorrectly marked as related and thus not randomly assigned."
The Justice Department and JetBlue declined to comment.
In the case filed on Tuesday, the Justice Department said the merger of JetBlue and Spirit would "combine two especially close and fierce head-to-head competitors."