Japan's coast guard said it had detected on Saturday what could be a ballistic missile that fell into the sea.
It appeared to have fallen outside Japan's exclusive economic zone, public broadcaster NHK said, citing the military.
The missiles were launched from an area near the capital Pyongyang, towards the sea off the country's east coast, South Korea's Joint Chiefs of Staff said in a statement.
North Korea has test-launched a wide range of ballistic and cruise missiles for more than two decades in a push to develop the means to deliver nuclear weapons, which it is believed to have successfully built.
As a result, Pyongyang has been under multiple UN Security Council sanctions since 2006 but it remains defiant, despite severe obstacles they created to its trade, economy and defence.
South Korea and Washington this week launched the annual major drills in South Korea, which they say are purely defensive, aimed at testing readiness against military threats from North Korea.
Hundreds of US and South Korean troops conducted river-crossing drills on Saturday with hardware including tanks and armoured combat vehicles, overseen by the commander of their combined forces.
The US military has about 28,500 troops and squadrons of fighter jets stationed in South Korea.
North Korea frequently displays its anger at such exercises, saying they are "dress rehearsals" for armed aggression against it by the allies.
On Thursday, South Korean Prime Minister Kim Min-seok met US President Donald Trump in Washington to discuss ways to reopen dialogue with the North.
Trump is eager for any opportunity to sit down with North Korean leader Kim Jong-un, South Korea's Kim told reporters.
