The North fired one missile from an air base in the eastern port of Wonsan Wednesday morning, but the launch "is believed to have failed", Seoul's defence ministry said in a statement.
"We are in the process of analysing what type of missile it was," it added.
The statement came after Japan's Kyodo news service, citing an unidentified government source, said the North might have launched several missiles and that they were a failure.
It is on a quest to develop a long-range missile capable of hitting the US mainland with an atomic warhead, and staged two nuclear tests and multiple missile launches last year.
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Earlier this month it launched a flight of four ballistic missiles, with three landing provocatively close to Japan in what Pyongyang described as practice for attacks on US military bases in Japan.
On Sunday, the North's leader Kim Jong-Un personally oversaw and hailed a "successful" test of what Pyongyang said was a new rocket engine -- which can be easily repurposed for use in missiles.
The developments come as Seoul and Washington hold large-scale annual joint military exercises that always infuriate Pyongyang, which sees them as a rehearsal for invasion.
Analysts' opinions are varied on how advanced the North's missile technologies are but many agree that Pyongyang has made significant progress in recent years.
The engine test was apparently timed to coincide with a recent Asia trip by new US Secretary of State Rex Tillerson, who warned that regional tensions had reached a "dangerous level."
Washington would drop the "failed" approach of "strategic patience" with Pyongyang, Tillerson said, warned that US military action was an "option on the table" if necessary -- a sharp divergence from China's insistence on a diplomatic approach to its neighbour, which it has long protected.
Pyongyang insists that it needs nuclear weapons for self-defence against "hostile enemies" including the South and its ally the US.