The North was probably showing its determination to push ahead with missile development in the face of global pressure to rein it in and "to pressure the (South Korean) government to change its policy on the North", South Korea's joint chiefs of staff spokesperson Roh Jae-cheon said.
The command tracked the missile for six minutes before it fell into the Sea of Japan, in what is known as Japan's exclusive economic zone. The South Korean army strongly condemned Pyongyang, saying its continuous provocations "will be facing strong punishment from our military, the South Korea-U.S. alliance, and the global community".
Earlier in May, North Korea tested the Pukguksong-2 intermediate range ballistic missile.
North Korea has fired what appears to be a short-range Scud missile off its east coast, South Korea's military has said.
Fresh from his global visit to Saudi Arabia and meetings with European leaders to discuss NATO, Mr Trump is using Twitter again to comment on world affairs.
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According to Yonhap, North Korea recently developed a new missile called the Scud-ER (extended range), capable of flying up to 1,000 kilometers - as far as Japan. Such language had been the source of anxiety for South Koreans and some on Capitol Hill alike, and a group of U.S Democratic congressmen of the House of Representatives in a letter to Trump last week reminded him he would need congressional approval for any pre-emptive strike on North Korea. In the event of war, they would bring danger to China and to Russian Federation as well. Mattis declined to say what kind of action from Pyongyang would constitute a "red line" for Washington, saying the administration needs "political maneuver room".
North Korea led by headstrong leader, Kim Jong Un, has continued to ruffle feathers by carrying out missile tests in defiance of UN sanctions warnings and United States threats of possible military action.
Last year North Korea also conducted two nuclear tests, and analysts have been predicting that Pyongyang is preparing for another one, based on activity around the country's nuclear test facility.
Mr Trump has in the past commended China for its efforts to rein in the North Korean nuclear weapons and missile testing programme. "It also clearly violates resolutions adopted by the United Nations Security Council".
But China, the North's main trade partner and ally, has made it clear that the push for diplomatic talks - not imposing more sanctions - was the priority.