The third missile was not destroyed but did not reach its target, the air force said without going into further detail.
The combat drones were headed towards the western region of Khmelnytskyi, the air force added. The target was not identified, but the region is home to a large air base.
The air force noted the missiles were shot down over the southern region of Mykolaiv, while the drones were downed in seven provinces all over Ukraine.
Earlier on Wednesday, Russia’s defence ministry announced a frigate from its Black Sea Fleet launched an attack with four cruise missiles on Ukraine’s military infrastructure, but it was not clear when the attack took place.
The Russian defence ministry occasionally releases information after a delay.
Ukraine’s navy announced Russia’s three cruise missiles were launched from the Kherson region bordering the Black Sea, parts of which have been under Russian control since early in the war that Moscow started 21 months ago.