It said the projectiles appeared to be short-range ballistic missiles.
They were launched early on Saturday from Pyongan province towards the East Sea, also known as the Sea of Japan.
North Korea launched multiple missiles as part of firing drills earlier this month. The US and China have called on Pyongyang to return to talks on ending its nuclear and missile programmes.
On Saturday, South Korea's military said it was monitoring the situation in case there are additional launches.
Japan's coast guard confirmed a missile had landed outside the waters of its exclusive economic zone.