Pyotr Ivanov, the head of Mosgortrans, told a news conference: "We transported Chelsea and Manchester United fans from Moscow airports. Unfortunately, Manchester United have not paid in full."
In the largest invasion by foreign soccer fans the city has ever seen, around 40,000 British fans traveled to the Russian capital for the final. United lifted the trophy after a dramatic penalty shoot-out.
Moscow's transport service provided around 1,000 buses to ferry fans to and from the city's airports.
The final was accompanied by a massive security presence, with thousands of police deployed on the streets, and the city metro system was kept running for several extra hours.
Manchester United is the richest soccer club in the world according to Forbes Magazine, which in April put the club's value at $1.8 billion, up from $1.5 billion when U.S. investor Malcolm Glazer bought the club in 2005.