"Unfortunately, decisions made in the recent months and even years, give grounds to doubt full objectiveness and lack of bias in the European court," Alexander Konovalov said.
The Strasbourg court made two decisions against Russia on Thursday, obliging the country to pay a total of $238,500 in compensation in various cases.
The court ordered Russia to pay 10,000 euros ($12,800) to Russian judge Olga Kudeshkina in connection with a violation of the right to freedom of expression, and 176,744 euros ($225,700) in compensation to the relatives of four people who went missing in Chechnya between 2002 and 2005.
The minister also said, however, that many decisions made by the Strasbourg court helped Russia to take notice of "really important" issues, such as violations of human rights on a range of matters.
Russia has lost the majority of cases brought against it in the Strasbourg court. In 2008, the court ruled against Russia 245 times. Overall, around 20% of all complaints made to the Court in the past decade have involved Russia.
