North Korea fired a short-range missile into the sea on Saturday, the 15th time it has launched rockets this year, the South's Yonhap news agency reported.
South Korea's Joint Chiefs of Staff in a statement said the North "fired a short-range missile presumed to be a Scud-type one into the East Sea" (Sea of Japan) at 09:40 pm (12:40 GMT).
The missile, with an estimated range of 500 kilometres (300 miles), was launched in a northeastern direction from Jangsan Cape in North Korea's western coastal region near the de facto sea border between the two states.
"We are analysing the motive of its missile launch, and we have maintained high-level readiness against its possible additional firing," Yonhap quoted the JCS statement as saying.
Pyongyang had not imposed a no-fly, no-sail zone ahead of the launch, which was the sixth ballistic missile firing this year, the news agency said.
The Japanese prime minister's crisis management centre said the launch was "extremely problematic" for aircraft and shipping and added on its Twitter account that it would protest to North Korea.
United Nations resolutions bar North Korea from conducting any launches using ballistic missile technology, with the UN Security Council earlier this month condemning Pyongyang for its recent firings.
"Our military sees the launch by North Korea, conducted while expressing its will to participate in the upcoming Incheon Asian Games, as part of its traditional dual strategy of engagement and pressure," the JCS said.
"We cannot but doubt its sincerity in claiming that it expects national reconciliation."
Pyongyang has been playing hawk and dove in recent weeks, mixing its tests with peace gestures that have been largely dismissed by Seoul.
The two Koreas are currently trying to sort out logistics for the North's participation in the Asian Games, which begin in September in the South Korean city of Incheon.