Ukraine has targeted Crimea throughout Russia's offensive but attacks on military installations there have recently intensified as Kyiv vows to recapture the peninsula, which Moscow annexed in 2014.
"The headquarters of the fleet have been hit in an enemy missile attack," Mikhail Razvozhayev, the governor of Crimea's largest city Sevastopol, said on social media.
Razvozhayev said that missile fragments had fallen near a theatre and urged residents to stay clear of the site.
In a second post, he warned that another aerial attack could be imminent, urging residents of the city, which is home to more than 500,000 people, to remain indoors.
"Attention everyone! Another attack is possible. Please do not go to the city centre. Do not leave buildings," he said.
"Everyone who is near the headquarters of the fleet -- at the sound of the siren proceed to shelters," Razvozhayev added.
He said rescue workers were at the scene, adding: "Firefighters are taking all measures to eliminate the fire as soon as possible."
'Once again'
Russia's defence ministry said five missiles had been shot down by air defence systems.
It said one serviceman was missing, after initially announcing a death.
"I would like to thank the air force pilots once again" Ukrainian air force commander Mykola Oleshchuk said after the strike.
The peninsula is also contending with an "unprecedented cyberattack" on its internet providers, said Oleg Kryuchkov, an adviser to the Moscow-installed Crimea governor.
Ukrainian and Russian attacks in and around the Black Sea have increased since Moscow withdrew from an accord that allowed safe passage to civilian cargo ships from three Ukrainian ports.
Ukraine has urged its allies to provide its armed forces with long-range missiles so it can target positions deeper inside Russia-controlled territory.
Western leaders had hesitated over concerns Ukraine could target Russian territory and thereby escalate the conflict.
Both France and the United Kingdom had, however, supplied Kyiv's forces with the weapons.
Airfield struck
As part of the increasingly frequent barrages on Crimea, Ukraine said earlier this week it had struck a military airfield near the town of Saky.
A source in Ukraine's SBU security service said there were at least a dozen warplanes and Pantsir missile defence systems at the airfield when the attack took place.
The airfield also housed a training centre for operators of drones that Russia uses to target Ukraine.
The SBU source said that Ukraine had deployed a swarm of unmanned aerial vehicles which "overwhelmed Russian air defenses" and then launched Neptune cruise missiles.
Kyiv has also repeatedly targeted -- and hit -- the only bridge that connects the peninsula to the Russian mainland, on several occasions leaving damage that took weeks to repair.
The last major attack in July impacted the road section of the bridge, which can accommodate rail traffic and is also used to transport military equipment.
Russian officials said on Friday that traffic across the bridge had been temporarily paused.
Civilian maritime traffic was stopped earlier on Friday in Sevastopol, Russian-installed authorities said, without providing details.
Russia's defence ministry said its forces had shot down one guided missile and two drones that had targeted the peninsula.
© Agence France-Presse
