Japan said that the missile likely passed over its territory and has warned residents to take shelter, local media report.
South Korea and the US are analysing the details of the launch, the South's military said.
Last month, North Korea fired a missile over Japan in what Tokyo called an "unprecedented threat" to the country.
The missile launch comes just days after new sanctions were imposed on North Korea by the United Nations because of its weapons testing.
In response to the missile alert on Friday, South Korea's military conducted a ballistic missile drill in the Japan Sea, known as the East Sea, Yonhap news agency reports.
South Korea's presidential palace, the Blue House, has called an urgent National Security Council meeting.
File photo: North Korea says it has developed and tested a hydrogen bomb