Environmental groups say the pipeline will endanger the world's largest freshwater lake, Lake Baikal.
The 4,100-kilometer pipeline is to run to Russia's Pacific Coast, enabling Russia to increase oil exports to China, Japan, and South Korea.
The state-controlled Transneft company is building the $11 billion Kremlin-backed project.
Environmentalists had also argued that members of the regulatory agency that approved the routing had been pressured to ensure a favorable vote. Transneft denies any attempt to pressure the panel.