Polanski, who was awarded the Silver Bear for best director at the Berlin Film Festival, also took five other key prizes at the ceremony held in the Estonian capital, Tallinn, late Saturday.
Nominated in seven categories, the movie won the best director prize, best actor for Ewan McGregor, and best screenwriter went jointly to Robert Harris and Polanski.
"You have awarded a truly European venture. This is too much ... thank you very much," Polanski said in an acceptance speech through a Skype connection from an unknown location. "I wish to thank — before anything — this wonderful crew I had, a truly European crew."
It was not the first time that the Polish-born director has received recognition from the European Film Academy.
The 77-year-old Oscar winning director of movies like "Rosemary's Baby" and "Chinatown" was honored with a lifetime achievement award in 2006 in Warsaw, Poland.
In Tallinn, French composer Alexandre Desplat was awarded for best composer while his compatriot film editor Herve de Luze won the production designer prize for Polanski's movie, which was mainly shot in Germany.
"The Ghost Writer," about the memoirs of a politician, played by Pierce Brosnan, is loosely based on former British Prime Minister Tony Blair.
Its production was a tangled tale for Polanski.
As he was finishing the movie in September 2009 Polanski was taken into custody at Zurich airport by Swiss police at the request of US authorities to face prosecution in a 1977 child sex case. He had to finish editing the film while in Swiss prison before being released on house arrest.
In July, Polanski was freed after the Swiss government declined to deport him to the United States. But he still faces an Interpol warrant in 188 countries. Most European nations, including Estonia, have an extradition treaty with the United States.
McGregor, who played the ghostwriter, said he had a "fantastic time" while making the film.
"More than any other part I've played I feel like the director Roman Polanski had his hands really on my performance and is as worthy of this award as I am," McGregor told the audience through a video message from Thailand, where he is currently shooting a film.
Among other prizes at the academy's 23rd annual awards ceremony, Swiss actor Bruno Ganz was honored with a lifetime achievement prize handed out by German director Wim Wenders.
Ganz, 69, with a screen career that spans five decades with memorable performances in Wenders' "Wings of Desire" and "The American Friend," in which he costarred with Dennis Hopper. He is also remembered from his acclaimed performance as Adolf Hitler in the 2004 German drama "Downfall" that portrays the last days of the Third Reich.
French actress Juliette Binoche presented the European achievement in world cinema award to Lebanese composer and musician Gabriel Yared, who has written scores for "The English Patient" and "The Talented Mr. Ripley."
The prizes — the European equivalent of the US Academy Awards — have been presented since 1988 by the European academy to celebrate the continent's film industry as a European counterweight to the Oscars.
