Lowry is accused of throwing a ball at a female referee twice and also threatening her and challenging her to a fight at a game between NBA players on September 22, according to multiple reports Friday, including one from the Las Vegas Review-Journal.
The referee, 30-year-old InFini Robinson, was formerly a guard on the UNLV basketball team.
Lowry is scheduled to appear in court on February 2.
In a statement, Rockets general manager Daryl Morey said: "We are aware that a complaint has been filed in Las Vegas against Kyle. We will work to get clarity on the situation. As this is a legal matter we will not comment further."
Lowry, 25, has averaged 15.3 points, 10.0 assists and 6.2 rebounds in six games for the Rockets this season. He was sidelined for Friday's game against Oklahoma City because of a bruised foot.