The missile was fired from the Admiral Gorshkov warship in the White Sea and hit a naval target more than 400 km (250 miles) away, the defense ministry said, in its second test in a fortnight.
A short video clip showed the missile illuminating the night sky with a burst of white light.
The United States, China and North Korea are also involved in the contest to hypersonic missiles, the next generation of long-range weapons that are harder to detect and intercept. They travel at more than five times the speed of sound in the upper atmosphere, or around 6,200 km/hour (3,850 mph).
Putin announced an array of new hypersonic weapons in 2018, saying they could hit almost any point in the world and evade a US-built missile shield.