Shoigu and Austin held a phone conversation earlier in the day at the initiative of the US side.
"During the conversation, it was noted that the flights of US strategic unmanned aerial vehicles off the coast of Crimea were of a provocative nature, which created prerequisites for an escalation of the situation in the Black Sea zone," the ministry said.
Russia is not interested in such a development of events, but it will continue to respond proportionately to all provocations, the ministry said.
Major nuclear powers should act as responsibly as possible, including maintaining military communication channels to discuss any crisis situations, it was further underscored.
Touching on the recent Black Sea incident in which a US Reaper drone crash-landed as a result of engaging in sharp maneuvering, the Russian defense minister reiterated that the US was at fault for the development.
"The main attention was paid to the exchange of views on the causes and consequences of the incident with the crash of a US unmanned aerial vehicle on March 14 this year in the Black Sea," the ministry said of the Wednesday conversation.
"Shoigu indicated that the cause of the incident was the actions of the United States in non-compliance with Russia's declared flight restriction zone, established in connection with the conduct of the special military operation, as well as increased intelligence activities against Russia's interests," it added.
Earlier Tuesday, the US European Command claimed that a crash occurred over the Black Sea and placed blame on a Russian SU-27 aircraft; however, it was later detailed by the Russian Defense Ministry that the jets never came in contact with the drone nor used any airborne weapons on the surveillance craft.
Russian fighter jets had been dispatched to the vicinity of the drone after it was determined that the drone flight "was carried out with transponders turned off, violating the boundaries of the area of the temporary regime for the use of airspace, established for the purpose of conducting a special military operation, communicated to all users of international airspace and published in accordance with international standards," the defense ministry explained at the time.