"If our Russian colleagues agree for their flights to be inspected at a Bulgarian airport, we will grant them a permit," Bulgarian Foreign Minister Daniel Mitov told journalists.
His remarks came a day after Nato and EU member Bulgaria confirmed it had refused permission to an unspecified number of Russian aircraft to cross its airspace last week, angering Moscow.
There was no immediate reaction from Russia to Mitov's remarks.
Moscow had on Tuesday demanded answers from Bulgaria and Athens, suggesting both countries had denied permission for Russian planes to use its airspace.
But although Greece confirmed receiving a request from Washington to bar two Russian planes from crossing its airspace between September 1 and 24, it said Moscow had later decided to use an alternative route.
Washington has expressed concern following reports suggesting Moscow may be boosting military support to Syrian President Bashar al-Assad and had sent a military advance team to the war-torn country.
On Wednesday, Athens denied any rift with Moscow over the matter with the foreign ministry saying that "no displeasure or any other negative comment has been expressed from anyone."
Mitov said the European Council had imposed restrictions on the supply of certain goods and services to Syria which every EU member state was "obliged to implement".
"We had enough information to give us reasons to believe that there is a discrepancy between the declared purpose of the flights and the real delivery, meaning that we would not issue a permit," he added.
Using Bulgarian and Greek airspace allows Russian planes to bypass Turkey and Iran on their way to Syria.
In 2012, Turkish warplanes forced a Damascus-bound passenger plane from Moscow to land and searched it on suspicion it was carrying equipment that breached civil aviation rules.
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