NTV said that the officer, who holds one of the top posts in Vnukovo Airport's customs department, was caught accepting a $1,000 clearance bribe from a passenger.
According to police, this is the highest-ranking civil servant to have been arrested in Moscow in the past 15 years.
Investigators believe the detainee to be the leader of a group of customs officers involved in extortion.
"We have detained the main organizer of all [criminal activities] that have been taking place in recent years in Vnukovo Airport's customs bodies," an investigator told NTV.
The man was detained in a police raid that is part of a current nation-wide crackdown on bribe-taking and extortion in customs services.