Gen. Ahmad Vahidi's comments came a day after Russian President Dmitry Medvedev issued a decree on the ban, which also prohibited exports of tanks, aircraft and sea vessels to Iran.
Vahidi said Russia was at risk of humiliating itself for caving to international pressure by banning the sales of the sophisticated systems that could boost Iran's ability to defend itself against airstrikes.
"We think Russia should show it has an independent stance in choosing its relations with other countries as well as on international issues," he said in an interview with Iranian state TV.
Tehran is in a tense standoff with the US and other nations over its disputed nuclear program. Russia also has recently shown increasing frustration over Iran's policies.
Moscow signed a 2007 contract to sell the systems. Israel and the United States have objected to the deal, and no such missiles have been delivered yet.
Russia has said United Nations sanctions would prevent it from delivering the S-300s to Iran.
The S-300 is capable of shooting down aircraft and missiles at ranges of over 90 miles (144 kilometers) and at altitudes of about 90,000 feet (27,432 meters).
Vahidi insisted the Russians were obliged to implement the 2007 contract.
"They have not done it so far," he said.
He also played down the importance of the deal, saying it was "not vital" because Iran will build a similar system in the future.
"God willing we will have production of long range anti-aircraft missiles on our agenda."
In June, Russia joined other members of the UN Security Council in imposing a fourth set of sanctions on Iran after Tehran refused to halt its uranium enrichment activities.
The US and its allies accuse Iran of trying to develop nuclear weapons. Iran denies the charge, saying its nuclear program is for peaceful purposes like power generation.
