Its predecessor, the S-400 system, has become a source of geopolitical tension with the United States actively discouraging countries to buy it, and, in the case of Turkey, unsuccessfully trying to persuade Ankara to return it.
Footage released by the defence ministry showed the giant truck-based system's launch tubes firing a missile at high speed into the sky at a testing ground in southern Russia.
Russia's state RIA news agency said it was the first time that the defence ministry had shown the S-500 system undergoing a live fire test.
Parts of the footage had been deliberately blurred or obscured to make it harder to examine the system in detail.
The ministry said the missile had successfully hit a "high-speed ballistic target".
"The S-500 anti-aircraft missile system has no analogues in the world and is designed to defeat the entire spectrum of existing and promising aerospace attack weapons of a potential enemy in the entire range of altitudes and speeds," the ministry said in a statement.
"Once the full test cycle is complete, the equipment plans provide for the delivery of the first S-500 system to the Air Defence and Missile Defence unit near Moscow," it said, without specifying a time frame.
The S-500 system, called Prometheus, is capable of destroying ballistic and cruise missiles, as well as planes and helicopters, and has an interception radius of around 600 km (373 miles), RIA reported.
Citing Deputy Defence Minister Alexei Krivoruchko last year, RIA said the S-500 system was slated for delivery by 2025, with state contracts due to be signed this year.
Tuesday's launch took place in the southern Astrakhan region at the Kapustin Yar training range, the defence ministry said.
The test comes a day after Russia tested a Tsirkon (Zircon) hypersonic cruise missile, a weapon President Vladimir Putin has touted as part of a new generation of missile systems without equal in the world.
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