The projectile was launched from South Hwanghae province around 7.50 a.m. (local time), Yonhap news agency quoted the JCS as saying. Further details are being analysed, the official said.
The launch came after North Korea test-fired two medium-range Rodong ballistic missiles and one shorter-range Scud missile on July 19 in an apparent protest against the decision between Seoul and Washington to deploy Terminal High Altitude Area Defence on South Korean soil.
Japan has also condemned and lodged an official protest with Pyongyang against the missile launch, saying the launch was in defiance of UN Security Council resolutions.
Defense Minister Gen Nakatani said the missile landed within Japan's exclusive economic zone in the Sea of Japan.
He said that his agency was currently "analysing the situation".
On July 8, South Korea and the US abruptly announced an agreement to deploy one THAAD battery by the end of next year.
One day after the announcement, Pyongyang test-fired a submarine-launched ballistic missile (SLBM) off its east coast to demonstrate against the THAAD deployment decision.
North Korean military has threatened to take "physical measures" against the THAAD deployment site.
China and Russia have strongly opposed to THAAD deployment in South Korea as it raises tensions in Northeast Asia.
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