Opponents of Matilda have gathered signatures against the film. Earlier this month, several hundred people gathered to outside a Moscow church, praying for the movie to be banned.
On Thursday, however, the Russian Culture Ministry finally announced that the film had received official clearance for release.
Nicholas II, Russia's last tsar, was canonised by the Russian Orthodox Church in 2000, and is still a divisive figure in Russia 100 years after his death.
As Russia marks the centenary of the year that saw Vladimir Lenin's Bolsheviks get into power, the film's trailer has shown intimate scenes involving Matilda Kshesinskaya and Nicholas II who was killed by the Bolsheviks in 1918.
Many of the film's critics see it as blasphemy against the emperor, who is still greatly revered by the Russian Orthodox Church.
Both the film's defenders and its critics have appealed to the Kremlin which has not publicly entered the debate.
Vyasheslav Telnov, the head of the Russian Culture Ministry's film department, said: "There is no censorship in Russia, and the ministry of culture stays away from any ideological views of beliefs. A feature film can't be banned for political or ideological motives."
Nevertheless, the Russian Orthodox Church still exercises significant pressure in Russia. It has recently played a role in the shutting down of an exhibition displaying nude photos and the cancellation of a performance of the musical Jesus Christ Superstar.