According to a statement released by South Korea’s Joint Chiefs of Staff, the missile was launched off the North’s east coast in the Sea of Japan late on Tuesday.
The KN-11 missile was launched from waters near Sinpo and flew about 500km (300 miles) before falling into the Sea of Japan, the statement added.
Japanese Prime Minister Shinzo Abe said that Tokyo “strongly protested” the launch, which he referred to as a “grave threat” to his country.
Japan’s self-defense force would remain on alert in case of further launches by Pyongyang, he added.
The launch comes two days after South Korea and the US began annual military exercises that North Korea condemned as a preparation for invasion, and has threatened retaliation.
The North warned that “peace, security and relaxation of tension on the Korean Peninsula and in the region cannot be thinkable unless the US-South Korea aggressive joint military exercises are totally halted.”