Israel says it carried out the missile test that raised tensions over the Syrian crisis, in the Mediterranean Sea on Tuesday.
Russia said it had detected the launch of two ballistic "objects" in the Mediterranean Sea, heading east.
But after a time it became clear there was no sign of a missile strike on the Syrian capital Damascus.
Russia later said the objects had fallen into the sea and then Israel said it had carried out a test of a missile, used as a target in a United States-funded anti-missile system.
The Interfax news agency quoted a ministry spokesperson as saying the launch was detected by an early warning radar station at Armavir, near the Black Sea, which is designed to detect missiles from Europe and Iran.
The Russian Defence Ministry earlier criticised the United States for deploying warships in the Mediterranean close to Syria.
Russia says US claims unproven still
Russia says the United States has not proved its allegations that a chemical attack was launched by the Syrian regime on its own people.
Moscow continues to maintain last month's attack, which killed more than 1400 people, may have been staged by Syrian rebels to provoke outside intervention in the civil war.
Following a meeting between US ambassador to Moscow, Michael McFaul, and a senior Russian diplomat, foreign minister Sergei Lavrov says Russia remains unconvinced.