Russia's defence ministry said that an explosion aboard Moskva, the flagship of the country's Black Sea Fleet, "seriously damaged" the vessel.
Russia did not say the cause of the fire, but earlier Ukraine said it was struck by their own Neptune missiles.
Earlier in the war, Ukrainians stationed on Snake Island in the Black Sea defied an order to surrender from the ship, telling the Moskva to "go to hell."
Ukraine launched two Neptune anti-ship cruise missiles at Russia’s missile cruiser “Moskva” in the Black Sea, causing serious damage, the head of Odessa’s regional administration said on Telegram. It did not provide any evidence.
Russia’s defence ministry has confirmed the ship was “seriously damaged” and the crew completely evacuated “as a result of detonation of ammunition caused by fire” its state agency TASS reports. The ministry said the cause of the fire was being determined.
Moskva is the flagship of the Black Sea Fleet, reportedly leading the naval assault on Ukraine.
The 12,500 metric ton ship has a crew of around 500. Russian news agencies said the Moskva was armed with 16 anti-ship "Vulkan" cruise missiles, which have a range of at least 700 km.
Maksym Marchenko, governor of the region around the Black Sea port of Odesa, earlier said in an online post that two anti-ship missiles had hit the cruiser, but he did not provide evidence.
Last month, Ukraine said it had destroyed a large Russian landing support ship, the Orsk, on the smaller Sea of Azov to the northeast of the Black Sea. Moscow has not commented on what happened to the ship.
Russia's navy has launched cruise missiles into Ukraine and its operations in the Black Sea are crucial to supporting land operations in south and east Ukraine.
The Moskva missile cruiser was constructed in the early 1980s in what was then the USSR.
It was actually built in Ukraine's southern city of Mykolaiv, which has been regularly shelled in recent days by Russian troops.
The 186m-long vessel was the lead ship of theSoviet navy's Project 1164 Atlant class. It was initially called Slava, but later renamed Moskva (Moscow).
The cruiser - which became the flagship of the Black Sea Fleet in 2000 - played a key role during Russia's military campaign in Syria, which began in 2015.