|The missile is believed to be a Scud|
The missile was launched from around the eastern North Korean coastal town of Wonsan, the South's Joint Chiefs of Staff said in a statement.
It flew about 280 miles (450km) before landing in the sea in Japan's exclusive maritime economic zone.
There were no immediate reports of damage to planes or vessels in the area.
Japan's Prime Minister Shinzo Abe swiftly condemned the test, saying: "We will never tolerate North Korea's continued provocations that ignore repeated warnings by the international community."
Japan's chief cabinet secretary, Yoshihide Suga, said the launch was "a clear violation of United Nations Security Council resolutions".
Mr Suga added: "Japan absolutely cannot tolerate North Korea's repeated provocative actions. We have strongly protested to North Korea and condemn its actions in the strongest terms."
Mr Trump wrote: "North Korea has shown great disrespect for their neighbor, China, by shooting off yet another ballistic missile...but China is trying hard!"
There was no immediate comment from the North's state controlled media.
Earlier on Sunday, North Korea tested a new anti-aircraft weapon system that Kim Jong Un says will "completely spoil the enemy's dream to command the air".
Read Also: North Korea tests weapon that will 'spoil enemy's dream'
Pyongyang said glitches detected in an earlier test have been "perfectly overcome", paving the way for the weapon to be mass produced and deployed nationwide.
State media says the system is designed to "detect and strike different targets flying from any location" - and footage showed the drill taking place.
Kim Jong Un's mood was brightened after the test in sunny North Korea
Three top officials accompanied the leader for the launch - including a veteran rocket scientist, a former air force general and the head of the blacklisted agency which is believed to be developing North Korea's missiles and nuclear weapons.
Last Monday, the secretive state said it had successfully tested an intermediate-range ballistic missile that met all technical requirements and could also be mass produced, but experts have questioned the extent of the country's progress.
A day later, the head of the US Defence Intelligence Agency said North Korea is on an "inevitable" path to obtaining a nuclear-armed missile capable of striking America if action is not taken.
However, Western experts believe Pyongyang is a few years away from successfully developing such a weapon.
This is the 12th ballistic missile test to be carried out by the North this year, and such actions have created tensions with Washington in recent months.
The reclusive nation has continued with its programme despite painful UN and unilateral sanctions - and described such punishment as an infringement of its right to self-defence.
Pyongyang maintains nuclear weapons are necessary to counter US aggression, but America denies it has any intention to attack the North.