In an open letter published by Kommersant broadsheet, more than 30 academics slammed Alexander Bortnikov, the head of the FSB security service - the successor to the feared KGB - for seeking to legitimise the mass purges known as the Great Terror.
Historians estimate about one million people perished in Stalin's purges in the 1930s out of around 20 million who died under his three-decade rule before his death in 1953.
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In an interview with Russian government newspaper Rossiiskaya Gazeta published this week Bortnikov said the archives show that "a significant part" of the criminal cases of that period "had an objective side to them".
He said he did not want to "whitewash anyone" but pointed to "links of coup plotters to foreign security agencies".
The interview was published to mark 100 years since the establishment of the Cheka, the Soviet Union's first secret police service, created to stamp out opposition to Bolshevik rule.
President Vladimir Putin - himself a former KGB officer - will run for a fourth Kremlin term in a March presidential election in a move expected to extend his rule until 2024 and cement his status as the longest-serving Russian leader since Stalin.
Many liberals have expressed concern that the Kremlin will tighten the screws on civil society even further following Putin's expected re-election.
In their open letter, the Russian scientists expressed fears that the "revision" of the role of the Soviet-era secret police could be intentional and called on the general public to join their protest.
"Apparently for the first time since the 20th Congress of the Communist Party held in 1956 one of the top functionaries of our state justifies mass purges of the 1930s-1940s which were accompanied by wrongful sentences, torture and executions of hundreds of thousands of innocent compatriots," they said in the letter.
Soviet leader Nikita Khrushchev used a secret session of the 20th Congress of the Communist Party to denounce the horrors of Stalin's rule.
The letter said that Bortnikov had failed to denounce the arrest or murder of millions of Soviet people including scientists and senior army commanders.
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"The goal of Mr Bortnikov's wide-ranging interview is not clear to us," said the letter published on the website of the respected newspaper late Friday.
"What is it? A recommendation to a new president? Nostalgia for bygone times or the propaganda of a new doctrine?" the letter added.
"In any case we firmly protest the revision of perceptions about the inhuman and anti-popular nature of the purges and call on all sensible people - who do not wish upon their children to relive the horrors of the 1930s - to join our protest."
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