“The details of the attack will be revealed as soon as possible and the result is dozens of dead and wounded occupants, including senior fleet commanders,” the Ukrainian army said.
Lt Gen Kyrylo Budanov, head of Ukraine’s military intelligence, said that the attack coincided with a meeting of top Russian generals and admirals in the building.
“Among the wounded is the commander of the group, Colonel-General [Alexander] Romanchuk, in a very serious condition. The chief of staff, Lieutenant General [Oleg] Tsekov, is unconscious,” Lt Gen Budanov told Voice of America.
Romanchuk is the commander of Russian forces along the southern frontline in Ukraine and Tsekov is commander of ground forces usually based in Arctic Russia.
Budanov said that nine people had been killed in the attack and 16 injured but he did not confirm internet speculation that Admiral Viktor Sokolov, commander of Russia’s Black Sea Fleet, was one of the dead.
Neither the Russian Ministry of Defence nor well-connected Russian bloggers have commented on casualties from the strikes.
Ukraine has killed several Russian commanders in missile strikes, but Friday’s attack is one of its most high-profile.
John Foreman, a former British military attache in Moscow, said that the missile strikes showed a typical lack of care by Russian commanders.
“Another self-inflicted disaster for the incompetents of the Russian Black Sea Fleet,” he said.
Co-ordinated Ukrainian missile strikes, electronic attacks and special forces raids on occupied Crimea have intensified over the past month. Analysts have said that Ukrainian commanders want to prove to their Western allies that they can take the fight to the peninsula before winter weather bogs down their forces along the frontlines.
They have mocked Russian air defence systems for failing to protect Sevastopol from attack.
Video of the attack showed that there had been no warning and no air raid siren. Tourists filmed the missiles hitting the headquarters in the middle of the city.
Ukrainian commanders have said that one of the main aims of the attacks is to erode confidence in the Kremlin.
And in online chatrooms from Sevastopol, residents complained about the lack of planning by the authorities.
“At the Fleet’s headquarters! In the centre of the city!” one user wrote. “When will everybody wake up?”
On Saturday, Russian news reports said that at least two air raid warnings had gone off in Sevastopol and one Ukraine missile had been shot down.