Polanski, 77, won for the film "Ghost Writer;" but didn't attend the ceremony Saturday in Tallinn, the capital of Estonia, the BBC reported.
He instead appeared via an Internet video link.
"You have rewarded a truly European venture," Polanski said from his home in Paris.
Scottish actor Ewan McGregor took best actor for his role in the film about a writer hired to "ghost" write the memoirs of a British prime minister.
He also appeared via an Internet link from Thailand, where he is working on another project.
Polanski was also honored for the screenplay, which he co-wrote with British novelist Robert Harris.
The film, released in the United Kingdom as "The Ghost in the U.K.," also took awards for production design and musical score.
Polanski remains wanted in the United States on an arrest warrant related to his 1977 conviction for unlawful sex with a 13-year-old girl.
The "Ghost Writer's" co-producer, Timothy Burrill, accepted Polanski's awards.
"Obviously I'm thrilled for Roman," Burrill said on the BBC News Web site following the event in Estonia.
The Israeli war film "Lebanon" won for its cinematography.
Lifetime achievement awards went to Lebanese composer Gabriel Yard and German actor Bruno Ganz.