File Photo: Russian President Vladimir Putin with Sevastopol Governor Mikhail Razvozhayev. (Photo courtesy of official Kremlin Twitter account)
"Ships of the Black Sea Fleet are repelling a UVA (unmanned aerial vehicle) in Sevastopol bay," Sevastopol governor Mikhail Razvozhayev said on Telegram.
"No facilities in the city have been hit. The situation is under control."
City authorities later said that the harbour was "temporarily" closed to boats and ferries.
Russia annexed the Crimea peninsula from Ukraine in 2014.
Its forces attacked Ukraine from several directions in February this year, including from Crimea.
Earlier this week, Razvozhayev said that a drone had attacked a thermal power station near Sevastopol.
The Russian fleet stationed in the port had also been attacked by a drone in July.
The latest announcement came as Ukrainian forces press a counter-offensive to retake land in the country's Russian-occupied south.