The missile was fired on Monday from the Tongchang-ri region, near the North's border with China, the South Korean military said.
Last month North Korea said it had successfully test-fired a new kind of ballistic missile in a launch supervised by leader Kim Jong-un.
The nation is banned by the UN from any tests of missile or nuclear technology.
The test in February was condemned by the UN, the US, South Korea and Japan.
A South Korean military official said the latest launch, which took place at 07:36 local time Monday (22:36 GMT Sunday), was being investigated to determine the type of the projectile used.
North Korea has repeatedly said its space programme is peaceful but it is believed to be developing an intercontinental ballistic missile that could strike the US.
It is also believed to be working to make nuclear warheads small enough to fit on a missile.
North Korea has launched an unidentified missile which fell into the Sea of Japan, South Korea says.