According to a one-page filing in federal district court in Maryland, Michael Haak, the pilot in command of the plane, exposed his genitals in acts that began, continued and ended while flight 6607 on Aug. 10 was in the air.
The document, which was dated Friday, did not indicate the circumstances and who might have witnessed the incident.
The brief filing doesn’t indicate if Haak has a lawyer.
A Southwest spokeswoman told The Associated Press that no passengers witnessed the incident; the pilots were the only people aboard aware of the incident.
The airline spokeswoman added Haak left the airline before the company was aware of the incident. Since learning of the allegations, she said, Southwest cooperated with investigators.
The Associated Press contributed to this report.