Ukraine claimed responsibility for a missile attack that struck the headquarters of Moscow's Black Sea fleet in annexed Crimea Friday, sparking a huge fire and leaving at least one Russian serviceman missing.

The strike on the symbolic heart of Russia's Black Sea fleet marks a major blow for Moscow, which has suffered a string of attacks on the strategically important port in recent months.

Russia's defence ministry said one serviceman was missing following the attack, after having initially reported that a serviceman had been killed.

"The historic headquarters of the Black Sea Fleet were damaged," it said, claiming air defence had shot down five missiles.

But Ukraine claimed that at least nine were killed and 16 injured, including the commander of the group, Col Gen [Alexander] Romanchuk. 

Plumes of thick smoke could be seen pouring out of the Russian naval headquarters, footage shared on social media showed, while officials said missile fragments had fallen close to a nearby theatre.

"The headquarters of the fleet have been hit in an enemy missile attack," said Mikhail Razvozhayev, the Russian-installed governor of Sevastopol, Crimea's largest city.

Ukraine confirmed the strike had hit Moscow's naval command base on the peninsula, which Kyiv has vowed to take back since it was annexed by Moscow in 2014.

"Ukraine's defence forces launched a successful attack on the headquarters of the command of the Black Sea Fleet of Russia in the temporarily occupied Sevastopol," the Ukrainian army said on Telegram.

A spokesman for the Ukrainian navy told AFP the attack appeared to be a "missile hit", but declined to confirm the navy's involvement.

"These measures will continue in the future," the spokesman added.