Bulgaria's foreign ministry said it suspected the aircraft were not carrying aid, as Russia claimed.
Betina Zhoteva, a spokesperson for the ministry, said Bulgaria had not come under pressure from its Nato allies.
Russia has been a key ally to Syrian president Bashar al-Assad during his four-year civil war with rebels groups.
"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," said Ms Zhoteva.
She said the decision to deny the Russian aircraft permission was taken late last week but did not give details about how many planes were involved.
Bulgaria's decision raises the diplomatic stakes; a clear signal from a Nato member that suspicions about Russia's activities in Syria are growing.
It comes against a backdrop of various reports of new Russian weaponry seen on the ground in Syria, along with unsubstantiated claims that Russia is pushing in advisers and possibly even some troops to bolster the Assad regime.
The denial of the use of Bulgarian air-space will annoy Russia but it has a perfectly feasible alternative option, routing over the Caucasus and Iran.
Vladimir Djabarov, vice-president of Russia's foreign affairs council, told state press agency Tass that the aircraft contained only "humanitarian cargo".
It is "not profitable to transport weapons by plane", he added.
Bulgaria's actions follow news on Monday that the US asked Greece, another Nato member, to ban Russian supply flights to Syria from its airspace.
US Secretary of State John Kerry on Saturday phoned Russia's foreign minister to express concern over reports of Russian military build-up in Syria.
Russia and the US disagree sharply on Syria. While Russia has backed the Syrian government, and provided it with arms, the US wants to see the removal of Mr Assad.
Bulgaria refused Russian aircraft permission to cross its airspace late last week, amid fears that Russia is boosting its military support to Syria.