It was not immediately clear what danger, if any, the launch on Tuesday posed to the China Southern Airlines aircraft travelling from Tokyo to Shenyang, China.
But Seoul Defence Ministry spokesman Kim Min-seok called it a "serious threat" that Pyongyang failed to notify international aviation authorities of its launch plans in the area.
He said the plane was travelling at an altitude of six miles, while the projectile's peak altitude was 12 miles. He said the flight passed through the area about five minutes after the projectile hit the water.
A North Korean army spokesman said rocket drills conducted from February 21 until Tuesday were part of regular training.
He said neither regional security nor the international navigation were in danger because the North took "scrupulous advance security measures for flight orbit and targets in the designated waters".
A Chinese Foreign Ministry spokesman called for all sides to refrain from provocations. The North is angry at joint US-South Korean military exercises.