North Korea launched a ballistic missile from its west coast towards the Sea of Japan, and it likely landed outside Japan's exclusive economic zone, Japan's top government spokesman said earlier.
Chief Cabinet Secretary Yoshihide Suga said it did not cause damage to ships or aeroplanes.
The rocket was fired from a location near Pukchang, north of Pyongyang, and flew about 500km (310 miles) eastward, South Korea's Office of Joint chiefs said in a statement.
White House officials travelling in Saudi Arabia with President Donald Trump said the system, last tested in February, has a shorter range than the missiles launched in North Korea's most recent tests.
"We are aware that North Korea launched an MRBM. This system, last tested in February, has a shorter range than the missiles launched in North Korea's three most recent tests," a White House official said.
China had no immediate comment while both South Korea and Japan called emergency meetings of top officials.
"South Korea and the United States are closely analysing the launch for further information," South Korea's Joint Chiefs of Staff said in a statement.
"Our military is closely monitoring the North Korean military for any further provocation and maintaining readiness to respond."
In pictures: North Korea marks the Day of the Sun
Show all 16
On Saturday, North Korea said it had developed the capability to strike the US mainland, although Western missile experts say the claim is exaggerated.
"The US mainland and the Pacific operational theatre are within the strike range of the DPRK and the DPRK has all kinds of powerful means for annihilating retaliatory strike," North Korea's state KCNA news agency said.
North Korea's official name is the Democratic People's Republic of Korea (DPRK).
Join our commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies
Join our commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies