The pipeline, due to run from Eastern Siberia to the Pacific coast, would hook round the northern end of Baikal -- the world's deepest lake and home to hundreds of endemic species including a rare fresh water seal. State monopoly Transneft says it will take all possible precautions to make the pipeline safe, but the scientists said nothing could protect it from the frequent earthquakes that afflict the zone and make the lake wider every year.
"No one can guarantee that there won't be an earthquake ... and that cannot but pollute Baikal," said Gennady Chegasov, who led a group of scientists that investigated the project for Russia's environmental watchdog.
"No engineer can guarantee there won't be ruptures."
Baikal, called the "Jewel of Siberia", is sacred to Russian environmentalists since protests over a proposed factory on its shores sparked the birth of the country's green movement in Soviet times.
Chegasov said his appraisal of the pipeline had yet to be approved by managers of the Rostekhnadzor environmental watchdog. If they back his assessment, Transneft will have to seek a new route for the $11.5 billion line.
He feared vested interests might cause his report to be quashed, considering how much money was at stake, and had decided to take the unprecedented step of going public with the report before its approval.
Officials frequently accuse activists who oppose big state projects of trying to sabotage Russian interests, and in July President Vladimir Putin himself said green groups trying to stop the pipeline were in the pay of foreign competitors.
Chegasov said he could rebut such allegations in court.
He said he understood the pipeline was necessary to diversify sales of Russia's key export, but said even the money earned from new markets in China and Japan could not justify the risk of polluting Baikal.
"By not building this further away from the lake we are saving $2 billion but we are risking the trillions of dollars that Baikal is worth," said Sergei Kolesnikov, who represents one of the regions near Baikal in the State Duma lower house of parliament and is vice-chairman of its science committee.
"For the sake of $2 billion we are risking the future."
Irina Maximova, a specialist on Baikal from the Russian Academy of Scientists, said the lake had 3,000 endemic species and was renowned for the purity of its water.
Any oil spill would destroy most species since they live in shallow water, she said, and particularly harm the Baikal seals.