"The patriarch gave this order when he was alive," Father Vladimir Vigilyansky told RIA Novosti.
The body of Alexy II, the Patriarch of Moscow and all Russia, will be brought to the Cathedral of Christ the Savior later on Saturday, where it will lie in state through the night.
Alexy II, who led the Russian Church for 18 years, died at the age of 79 in his residency near the capital on Friday morning.
A senior church official said earlier that heart failure was believed to be the cause of death. The patriarch was known to have suffered from health problems in recent years.
Alexy II became patriarch of the Russian Orthodox Church in 1990, shortly before the collapse of the atheist Soviet Union, and presided over a religious revival in Russia, with thousands of churches and monasteries being restored and hundreds of new ones built across the country.
Under his leadership, Russia's last tsar, Nicholas II, and his family shot by the Bolsheviks in 1918, were canonized as well as many New Martyrs who suffered under communism.
In 2007, he signed a reunification act with Metropolitan Laurus, head of the Russian Orthodox Church Outside of Russia (ROCOR), after almost 90 years of separation. The foreign branch broke away in 1921, after accusing fellow clergymen in Soviet Russia of collaboration with the country's communist regime.