Klimas was accused of exposing himself to a 20-year-old man at around 8:30 a.m. in the Union Turnpike station.
Police say the victim, who alerted police of the alleged exposure, told investigators that he has an ongoing relationship with the captain, who is assigned to the Transit Bureau's Special Operations District.
Klimas, a veteran of at least 20 years, is married with children and lives in New Hyde Park. He denied the charges and is cooperating with an Internal Affairs investigation.
Klimas was previously accused of a similar on-duty incident, but his alleged victim in that case, a teen, was determined not to be credible.
