It was the latest in a string of Russian refusals for the Dalai Lama to enter the country.
"The Dalai Lama is respected in our country as a leading religious activist, with many followers in our country," the foreign ministry said in Moscow on Tuesday.
But "we are obliged to consider Russia's national interests when considering a visit by the Dalai Lama," a ministry statement said.
Agreements with China oblige Russia "to support the policies of the Chinese side on points of China's government sovereignty and territorial integrity," the statement said.
"As is well known, the Dalai Lama's international activities are viewed negatively in China, where they are considered separatist," it said.
"We are obliged to consider Russia's national interests when considering a visit by the Dalai Lama"
Russian foreign ministry
The Dalai Lama was invited to visit Russia's southern Buddhist republic of Kalmykia by its president Kirsan Ilyumzhinov in August.
In August 2002, Russia had refused to allow the spiritual leader to visit its mainly Buddhist republics of Buryatia, Kalmykia and Tuva.
Earlier, in September 2001, the Dalai Lama was forced to call off a visit to Mongolia after Moscow denied him a transit visa.
The Dalai Lama has visited Russia several times in the past following his first visit in 1982 and most recently in 1992.
He fled Tibet after a failed uprising against Chinese rule in 1959.