The historical drama shot in Chechnya details how the Soviets forcibly deported the whole Chechen nation and the related Ingush group - half a million people - from their homeland in the North Caucasus to Central Asia in the winter of 1944, accusing them of lacking loyalty to the state.
A culture ministry official condemned the film as a "historical falsification" in a letter shown to AFP by the film's scriptwriter and producer, Ruslan Kokanayev.
Titled "Ordered to Forget", the film was intended to mark the 70th anniversary of the deportations this year.
The culture ministry, which licenses cinema releases, singled out a massacre depicted in the film in which 700 people were burnt to death in the Chechen mountain village of Khaibakh in 1944.
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The ministry said it had searched three Russian state archives including the files of the NKVD security forces that carried out the deportations and Stalin's personal files.
"This allows us to conclude that claims of this 'event' are a historical falsification."
An adviser to Culture Minister Vladimir Medinsky, Larisa Khon, told the Kommersant daily the ministry had not taken a final decision on the film and would carry out a further expert assessment.
The ministry did not respond to a request for comment from AFP.