Officers interviewed Crespo upon his arrival but did not arrest him. No charges have been filed.
When asked by police at the airport about the accusation, the 37-year-old Puerto Rican singer said: "I don't recall doing that."
A message left by The Associated Press Wednesday for his publicist, Mayna Nevarez, was not immediately returned.
Because the incident took place over U.S. air space, the FBI is also investigating. Messages left for the FBI office in Miami also were not immediately returned.
According to the police report, 52-year-old Patricia Perea of Canyon Gate, Texas, told police she was sitting next to the singer of the hit song "Suavemente." She said that about 15 minutes after the plane left Houston, Crespo covered himself with a blanket and began to masturbate, then exposed himself.
On March 16, Crespo married his manager, Maribel Vega, in Puerto Rico.
He was scheduled to fly to New York on Thursday to participate in commitments related to the city's Puerto Rican Day parade, which is usually in June.
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