The strikes on Wednesday evening came as both Moscow and Kyiv accuse each other of inflicting dozens of civilian casualties in a sharp escalation of attacks.
"Thirteen people were injured," including a Turkish citizen and a Georgian, the prosecutor general's office said.
"Two missiles hit a hotel in the centre of Kharkiv. There were no military personnel there. Instead, there were 30 civilians," Mayor Igor Terekhov posted on Telegram.
One of the wounded is in "very serious condition", he said, adding that "Turkish journalists are among the victims".
Oleg Synegubov, head of the Kharkiv regional military administration, said S-300 missiles were fired from the Russian frontier region of Belgorod, adding that a 35-year-old man was hospitalised in serious condition".
Several other buildings, including two apartment blocks, were also reported damaged in the latest strike.
"In addition to the hotel, residential buildings were affected -- one communal, one private, a car dealership and a manufacturing enterprise," Mayor Terekhov said.
Located about 30 kilometres (19 miles) from the Russian border, Ukraine's second-largest city has seen regular and often deadly aerial assaults.
Across the border, the Russian defence ministry said it had downed four Ukrainian drones over the Tula, Kaluga and Rostov regions.
Voronezh region governor Aleksandr Gusev also reported that a Ukrainian drone had hit "the roof of a non-residential building" overnight, although said there was "no harm done".
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