Russia is the biggest source of applications to the Strasbourg-based European court, a cause of embarrassment for some officials and a reflection of the low level of public confidence in the domestic judicial system.
Many lawyers and rights groups say Russian judges are not truly independent from the government and often ignore evidence in court cases to rule in favor of the prosecution.
"I generally agree that the Strasbourg Court, with all my respect for it, cannot and should not replace Russian justice," Medvedev, a former corporate lawyer, told a congress of Russian judges. "We must think how to transform the Russian judicial system to encourage citizens to make a choice in its favor."
The European Court of Human Rights hands down rulings if an applicant can demonstrate that he has not been given a fair hearing in courts in his?‰ home country. The Strasbourg court has handed down several unfavorable rulings on Russian cases, many of them relating to purported rights abuses by Moscow's security forces in the turbulent Chechnya region.
Those rulings irked Medvedev's predecessor, Vladimir Putin, who stepped down in May to become prime minister. Putin accused the Strasbourg court in January of making politicized decisions.
Medvedev has promised to modernize the Russian economy and make the country's political system more flexible to face the challenges of the 21st century. He has said an independent and respected judiciary is a crucial element of that drive.
"Perhaps in this sense, the courts are the most authoritative branch of power in the country," he told senior judges from across the country.
"Why is a de jure independent court often not de facto independent?" he asked the audience. "Why do judges not always make their personal choice in favor of impartiality and objective consideration of cases?"
Medvedev did not offer any specific solutions but said he wanted to consult with the judges on measures to make courts more independent, including steps to protect judges from outside pressure and give them better training.
He also said the courts need to be more transparent and that citizens should receive practical help on how to exercise their rights in court.
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