They were launched about 1pm local time from near Chongju in North Korea's North Pyongan Province, South Korea's Joint Chiefs of Staff (JCS) said in a statement on Tuesday.
The missile flew about 80 kilometres, the JCS said.
It is North Korea's first known missile launch since April 19, when the country test-fired several short-range ballistic missiles, which it said were equipped with cluster bombs.
In early April, Pyongyang also said it tested a new cluster-bomb warhead on a ballistic missile and an electromagnetic weapon, in a move analysts said was part of efforts to showcase the North's capacity to fight a modern war.
North Korean leader Kim Jong Un said in March his country's status as a nuclear-armed state was irreversible and expanding a "self-defensive nuclear deterrent" was essential to national security.
Despite UN sanctions on its nuclear weapons and ballistic missile programs since 2006, North Korea has accelerated efforts in recent years to build up its arsenal under Kim, drawing condemnation from South Korea, Japan and the United States.
South Korea's Foreign Ministry urged North Korea to respond to Seoul's peace overtures and efforts to reduce tensions.
Seoul would maintain its goal of the complete denuclearisation of the Korean Peninsula, while pursuing a phased and pragmatic approach to resolving the North Korean nuclear issue in close coordination with the international community, a spokesperson said in a press briefing on Tuesday.
with AP