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.
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.
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 scientists - who are all members of the Russian Academy of Sciences - 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.
The letter said that Bortnikov had failed to denounce the arrest or murder of millions of Soviet people including scientists and senior army commanders.
"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 yesterday.
"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."
"As a person born in 1937 I just want to issue a warning: 'People, be vigilant,'" he told Kommersant.
Andrei Soldatov, an expert on Russia's security services, called Bortnikov's interview "very dangerous."
"Over the past two to three years Putin has consciously been making the FSB an instrument of selective repressions," he told AFP, pointing to the current involvement of the security service in "nearly every" high-profile criminal case.
The clampdown could not only continue but expand to target more people in the future, he added.
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