Burkina's military rulers have deepened cooperation with Moscow, as the country looks to diversify its international allies following a coup last year.
Russia, which has grown more isolated since its Ukraine offensive, has in recent months discussed greater military cooperation with Burkina Faso.
Moscow has also pledged to deliver free grain to the African country, which is one of the world's poorest.
"Russian-Burkinabe relations are based solely on the principles of mutual respect and consideration of each other's interests, and in recent years they have gained positive dynamics," Shoigu said, according to the ministry.
The ministry published footage of Shoigu and Coulibaly shaking hands and holding a roundtable meeting with officials.
"I consider today's meeting to be another step in developing our friendly relations," Shoigu added.
Burkina Faso last year experienced two military coups -- both triggered in part by discontent at failures to stem a raging jihadist insurgency.
Since coming to power in September 2022, the ruling junta has distanced itself from France, its historic partner and former colonial power, and moved closer to Russia.
In October, Burkina Faso signed a deal with Russia for the construction of a nuclear power plant to increase the energy supply to the Sahel country where less than a quarter of the population has access to electricity.
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