Protocol 14 to the Convention, designed to simplify and speed up litigation, has been signed and ratified by all Council of Europe states except Russia, which said the document could encourage more politically motivated decisions against the country.
The protocol will only come into force once it has been ratified by all member-countries.
Vladimir Putin said it was the lower house's decision: "They argued that the new, simpler procedures at the Strasbourg court could damage the quality of proceedings."
The protocol to the Convention that established the European Court of Human Rights in Strasbourg was introduced to help the Court cope with the growing influx of complaints and to speed up investigations and trials, some of which last up to 10 years.
The State Duma, dominated by the Kremlin-backed United Russia party, declined to ratify the protocol last December on the grounds that the proposed norms contradicted the basic principles of the Convention, infringed on human rights, and could lead to discrimination against Russia.
Putin said the protocol proposed using case law and trying cases with only one judge. He also said Strasbourg court rulings on Russia were often politically biased, and cited the Ilashku case as an example.
Ilashku was found guilty on terrorism charges and sentenced to death by the unrecognized republic of Transdnestr, on Moldovan territory.
The breakaway region later handed the man over to Moldova as a goodwill gesture. But Russia, which brokers the resolution of the post-Soviet territorial conflict and has substantial influence in the region, and Moldova were found responsible for not interfering in the affair.
"Russia was accused of something it had no part in, and lawmakers highlighted the case," the president said. "That was a purely political decision that undermined trust in the international judicial system."
But he added "Russia will not curtail its cooperation with the Strasbourg court and will continue working there in its full capacity."
Rene van der Linden, chairman of the Parliamentary Assembly of the Council of Europe, said Thursday in the wake of his visit to Moscow that the State Duma's decision was a disappointment for him and the Council of Europe.
But he said he was confident the Russian parliament would heed his recommendations to continue debating the document and would ratify it in 2007.
