Tokyo attacked the launch of North Korea on the grounds that the country had violated UN resolution rules. Yoshihide Suga, Japan's chief cabinet secretary, said one of the rockets landed in the water of Chimane Prefecture. He also revealed that the two missiles were fired within minutes of each other. South Korea said the missile came from a submarine.
Suga said the first rocket crashed at 7:07 am local time (10:27 pm GMT).
South Korea's Joint Chiefs of Staff (JCS) said the launch took place around Wonsan in southeast Gangwon.
North Korea's launch comes a day after North Korea confirmed that it would maintain US labor-level negotiations this weekend.
It was North Korea's ninth launch since leader Kim Jong un met US President Donald Trump in June in the Demilitarized Zone between North Korea and South Korea.
Negotiations are expected to break months of deadlock over nuclear discussions.
They aim to break North Korea's nuclear and missile program.
Negotiations have stalled since Trump and Kim met in Vietnam in February.
These conversations ended without agreement.
Trump downplayed North Korea's series of short-range launches, saying that in September the US and North Korea "had no deal on short-range missiles" and that many countries are testing these weapons.
Lee Sung-yoon, professor of Korean studies at Tufts University's The Fletcher School, said: "North Korea has recycled its carrot and stick strategy against the US several times with great success."
This is when Japan warned that China's growing military might has become a greater threat to national security than North Korea, despite signs that Kim Jong-un armed his forces with nuclear-tipped ballistic missiles.
Over the past seven years, Tokyo has increased defense spending tenfold to combat the military advances of Beijing and Pyongyang, including defenses against North Korean missiles that can carry nuclear warheads.
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North Korea has conducted a series of short-range missile launches that Tokyo believes show that Pyongyang is developing projectiles to avoid its Aegis ballistic missile defenses.
China often dismisses concerns over its military spending and intentions, including a growing presence in the disputed South China Sea, and insists it wants only peaceful development.
The Defense White Paper said Chinese patrols in waters and skies near Japan are "a national security concern."
Last month, North Korea said its nuclear program could gain more freedom after Trump fired his security adviser John Bolton.
Trump and Kim were due to resume talks in September as the US tried to lead North Korea to denuclearization.
But the resignation of Bolton by the US president raised concerns about this goal.
The 70-year-old was one of Washington's toughest communicators about North Korea, before calling for preventive strikes and tough measures in the denuclearization process.
In its absence, observers believe the Trump administration's tough stance on the dishonest state could slow – opening the door for the regime to revisit its nuclear program.