The ministry had asked for his recall in a meeting with the Russian ambassador on Friday. The exact circumstances of the diplomat’s departure were not clear.
"A request has been made to the Russian institutions to recall their official by the end of Monday. According to foreign ministry information, the person in question has already left Bulgaria," the Bulgarian foreign ministry said in a statement, according to Reuters.
The Russian Foreign Ministry and its embassy in Sofia had no immediate comment.
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In a separate statement on Monday, prosecutors said an investigation, launched after a tip from the security services, established that a first secretary at the Russian embassy has been involved in intelligence activities for over a year.
Prosecutors said the diplomat has since last September held conspiratorial meetings with Bulgarians, including with a senior official with a clearance for classified information from Bulgaria, the European Union and NATO.
"The main goal of the meetings has been to obtain, for intelligence purposes, information that is considered a state secret, including through offering material benefits," the prosecutors said in a statement.
The prosecutors said they had closed the investigation despite reasonable grounds for espionage charges because the suspect had diplomatic immunity.
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Bulgaria, a loyal ally of Moscow in Soviet times, is now a member of NATO and the European Union but has close cultural and historic ties to Russia, which remains its biggest energy supplier.
According to a Ukrainian outlet Obozrevatel, the diplomat's name is Vladimir Rusyaev, that's according to his diplomatic sources who added that his post in the embassy had been traditionally reserved for GRU (military intelligence officers).
He is reported to have boasted of his affiliation with the intelligence agency during diplomatic events at the premises of Russia-friendly states.