Several missile tests were conducted over the past week by Pyongyang, but criticism was levelled at North Korean leaders after a test took place near a Chinese passenger plane on Tuesday.
The plane was en route to Shenyang, China, from Tokyo, carrying over 200 passengers, according to South Korean officials who publically decried the incident.
The North Korean projectile launched at 16:17 local time the plane passed through its trajectory just seven minutes later.
"An aircraft passed by as the ballistic missile fell. On a safety level, this is a serious issue of concern," said South Korea's Defence Ministry spokesman Kim Min-seok.
A Chinese foreign ministry spokesman said Beijing would seek more information, reported the BBC.
"There were no accidents, but a very dangerous and serious situation could have occurred," said the spokesman.
The missile tests coincide with annual joint US-South Korea military drills, which North Korean leaders have criticised for being provocative.