"The planes were said to carry humanitarian aid but we had information -- that we had every reason to trust -- that the declared cargo was not the real one," foreign ministry spokeswoman Betina Zhoteva told AFP.
Zhoteva said the decision was taken late last week but did not give details about how many planes were concerned.
She said the decision was taken independently without pressure from NATO partners.
A Russian official refused to believe Bulgaria's decision was made without pressure from the US.
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"The fact that the Bulgarians are the first to respond (to the request from Washington) -- they will have that on their conscience," said Vladimir Djabarov, vice-president of the Russian foreign affairs council.
He told state press agency TASS that Russia was only supplying "humanitarian cargo" to Syria, adding that it is "not profitable to transport weapons by plane".
Washington is concerned that Moscow could be increasing its military support to Assad, an issue raised by US Secretary of State John Kerry with Russian counterpart Sergei Lavrov at the weekend.
Russia had asked Greece to allow the passage of two planes between September 1 and 24. A Greek foreign ministry official told AFP they were examining the request and had yet to take a decision.