At an EU summit in Helsinki, Russian Transportation Minister Igor Levitin and European Commission President Jose Manuel Barroso signed an agreement to gradually reduce the charges in the years leading up to 2014, when they will be scrapped altogether.
Until now, European carriers have had to pay more than $300 million a year for flights over Siberia, the fastest route to destinations in China, Japan and Southeast Asia.
A long-standing dispute over over-flight fees, protested by the EU as a violation of the 1944 Chicago Convention on International Civil Aviation, has been a hurdle to Russia's bid to join the World Trade Organization.
Russia introduced the trans-Siberian over-flight tax in 1969, when long-range jetliners came into widespread use. Until then, European carriers could take their Asia-bound passengers only as far as Moscow, and then hand them over to the Russian national carrier Aeroflot.
Hosted by Finland, the current EU president, the summit was expected to launch negotiations on a new partnership agreement between Russia and the 25-nation club. But Poland has blocked the talks in response to Russia's unwillingness to lift a ban on Polish meat and plant products, imposed last year over alleged corruption in the EU newcomer's customs service.
Ahead of the Helsinki forum, Moscow also threatened to ban the import of EU meat after next year's accession of Bulgaria and Romania, which have both experienced outbreaks of mad cow disease in recent years.
The EU said the prospective measure could cost its agricultural exporters an estimated $2.2 billion in annual trade losses.
Energy is another major issue holding back EU-Russia partnership agreement talks, with Moscow reluctant to give foreign investors free access to its oil and gas deposits and export pipelines - something it would be obligated to do under the Energy Charter.
The EU has been pressuring Russia to ratify the charter, in effect since 1998, or to sign a transit protocol that would have Russian energy giant Gazprom give up its monopoly on transporting natural gas from Turkmenistan.
Along with trade, a new EU-Russia accord would also envisage closer cooperation in justice, external security and research matters. The old pact expires in 2007.
