The Russian governor of the region claimed that Ukrainian helicopters flew into Russia to attack the site at Belgorod, a logistics hub 40km from the border.
Russia claims that a fire that broke out at a fuel depot in the city of Belgorod early on Friday was the result of an attack by two Ukrainian military helicopters.
Kyiv later denied the accusation, having initially refused to confirm or deny it.
There was no independent confirmation of details about the incident.
“For some reason they say that we did it, but in fact this does not correspond with reality,” Oleksiy Danilov said on Ukrainian television on Friday.
“The fire at the oil depot occurred as a result of an airstrike from two helicopters of the armed forces of Ukraine, which entered the territory of Russia at a low altitude,” the Russian governor of the region wrote earlier on the messaging app Telegram.
Vyacheslav Gladkov claimed that two of the depot's workers were injured when the fire broke out at two in the morning local time.
Russia's Ministry of Emergency Situations claimed that more than 170 rescue workers had been sent to the depot.
Russia has reported shelling from Ukraine before, including an incident last week that killed a military chaplain, but not an incursion of its airspace.
Rosneft, which owns the depot, said it had managed to evacuate its staff.
It's the second-biggest state-owned energy company in Russia.