South Korea's Joint Chiefs of Staff said the military had detected two launches, the first at 5:05 am (2005 GMT) and the second around 10 minutes later.
"The short-range ballistic missile launched at around 05:05 flew approximately 600 km (372 miles)," it said, adding the second one travelled 120 km.
JCS spokesperson Lee Sung-jun said the second missile appeared to fly abnormally in an early stage of flight, adding that if it had exploded in mid-air, its trajectory indicates debris could have landed over North Korea.
Seoul's military has "strengthened surveillance and vigilance in preparation for further launches", JCS said in a statement.
North Korea is accused of breaching arms control measures by supplying weapons to Russia to use in its war in Ukraine, and Russian President Vladimir Putin held a summit with leader Kim Jong Un in Pyongyang in June in a show of unity.
The JCS's Lee declined to comment when asked whether the North's latest launch could have been a test of missiles intended for delivery to Russia.
The launch also comes after Pyongyang on Sunday denounced joint military exercises by South Korea, Japan and the United States, calling them an "Asian version of NATO" and warning of "fatal consequences".
The three-day "Freedom Edge" drills, which ran from Thursday to Saturday last week, included preparation in ballistic missile and air defences, anti-submarine warfare and defensive cyber training.
They also involved Washington's nuclear-powered aircraft carrier USS Theodore Roosevelt, Tokyo's guided-missile destroyer JS Atago and Seoul's KF-16 fighter jet.
Pyongyang has always decried similar combined exercises as rehearsals for an invasion, but Seoul defended the latest exercises, saying they were a continuation of defensive drills held regularly for years.
- Testing, testing -
Last week, North Korea claimed to have successfully tested a multiple warhead missile, but the South said that launch ended in a mid-air explosion.
Relations between the two Koreas are at one of their lowest points in years, with the North ramping up weapons testing while bombarding the South with balloons full of trash.
Pyongyang says those missives are in retaliation for balloons loaded with anti-regime propaganda leaflets sent northwards by activists in the South.
In response to the North's repeated launches, South Korea has fully suspended a tension-reducing military treaty. It also briefly resumed propaganda loudspeaker broadcasts, and conducted live-fire drills near the border.
North Korea is also currently holding a major party meeting, which was opened by leader Kim, state media said Saturday.
"In both North Korean politics and military policy, the best defence is often a good offence," said Leif-Eric Easley, a professor at Ewha University in Seoul.
"These missile launches are likely the Kim regime's way of compensating for recent failed tests, aiming to impress a domestic audience during ruling party meetings."
"Pyongyang is also determined not to appear weak while South Korea conducts defence exercises with Japan and the United States."
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