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"We confirm the fact that Russia is not shipping S-300s to Iran or to any other Middle East countries," the anonymous official was quoted as saying by the Interfax news agency.
"We cannot discuss prospects for arms shipments or dates for such shipments to Iran as well as to other countries. This is common practice among suppliers," he said.
The weapons that Russia had shipped to Iran were exclusively defense weapons and could not have destabilized the situation in the region, he said.
Earlier in the day, a high-ranking official of Russia's Federal Service of Military-Technical Cooperation said Russia had not delivered the S-300 air defense systems to Iran under a deal cut with the Islamic republic two years ago.
The S-300s are sophisticated, medium-range surface-to-air missile systems and have a longer range than the Tor-M1 systems.
Israel has urged Russia not to deliver such systems to Iran, alleging Iran wants to develop a military nuclear program and such a deal will not serve the interests of peace in the Middle East.
Tehran insists its nuclear program is solely for civilian purposes.