The missile was launched from a site near the northwestern city of Kusong at around 5:30 am (2030 GMT Saturday) and flew about 700 kilometres (435 miles), according to the South's Joint Chiefs of Staff.
"The South and US are analysing more details about the missile," it said in a statement without elaborating.
North Korea test-fired a missile from the same city in February with the missile flying more than 500 kilometres.
It is the second missile launch in around two weeks and the first since new South Korean President Moon Jae-In was sworn in on Thursday.
Moon has summoned an emergency meeting with his national security advisors, his spokesman said.
Japanese Prime Minister Shinzo Abe slammed the missile launch as "totally unacceptable" and a "grave threat" to Tokyo.
"We strongly protest against North Korea," he said.
The missile flew about 30 minutes before falling into the Sea of Japan (East Sea) between Japan and the Korean peninsula, said Tokyo's Chief Cabinet Secretary Yoshihide Suga.
One recent test by the North, held in early March, saw three missiles fall provocatively close to Japan, sparking alarm in Tokyo.
Tensions are running high on the Korean peninsula with Pyongyang and Washington exchanging hostile rhetoric.
The North has staged two atomic tests and dozens of missile launches since the start of last year in its quest to develop a missile capable of delivering a nuclear warhead to the US mainland.
Washington has suggested the military option is on the table, but President Donald Trump recently appeared to soften his stance, saying he would be "honoured" to meet the North's leader Kim Jong-Un.
Moon, who advocates dialogue with Pyongyang unlike his two conservative predecessors, also said in his inauguration speech that he was willing to visit Pyongyang "in the right circumstances" to defuse tension.
A senior Pyongyang diplomat also said Saturday the North would be willing to hold talks with the US if the conditions are right.
Choe Son-Hui, head of the foreign ministry's North American bureau that her country "will hold dialogue under right conditions" with Trump's administration.
Most experts have doubted that the North has developed an intercontinental ballistic missile (ICBM) capable of hitting the US mainland.
But many say the isolated nation has made a great progress in its nuclear and missile capabilities since Kim took power after the death of his father and longtime ruler, Kim Jong-Il, in 2011.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)