The source in the SBU security service said it had launched the joint operation with the navy, in Kyiv's latest aerial attack on Russian territory.
Russian officials earlier reported an industrial facility near the village of Chaltyr in the Rostov region bordering Ukraine was ablaze following a drone barrage, without elaborating.
"SBU drones and a Neptune missile targeted an ammunition and reconnaissance drone storage facility near the village of Chaltyr in the Rostov region," the Ukrainian source said.
It claimed the drones had overloaded Russian air defence systems, clearing the way for the missile to hit the military facility.
In a statement, the source added that the attack would limit Russian drone attacks on Ukrainian cities.
The head of the Rostov region, Yuri Slusar, said Ukraine had attacked the region overnight and that air defence systems had downed 16 drones near Chaltyr.
"In the village of Krym a fire is being extinguished on the territory of a production enterprise" following the attack, he said, adding later that the blaze had been extinguished.
Ukraine has claimed to have struck Russian military command posts in the occupied Donetsk region and the western Russian region of Kursk over recent days.
The military again claimed Friday it had hit a Russian command post in the occupied town of Svitlodarsk in a precision strike.
Russian officials had earlier said one person was killed and four others were wounded by a Ukrainian strike on Svitlodarsk.
Earlier this week Kyiv said it hit an oil depot that supplies a military airfield in Russia's Saratov region, some 500 kilometres (310 miles) from the warring countries' shared border.
Moscow has also ramped up its missile and drone attacks since winter, casting some of the strikes as retaliation for Kyiv's use of Western-supplied weapons on Russia.
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