Seoul's military claims the two projectiles have been fired into the sea.
It comes three days after Pyongyang revealed its troops conducted artillery drills near the disputed sea boundary with its neighbour.
Earlier on Thursday, Japan's coastguard said it was monitoring where the suspected missiles would land, but the defence ministry said they did not enter its airspace or its exclusive economic zone.
They were an apparent attempt by North Korea to pressure the US to make concessions in their stalemate over nuclear diplomacy.
In a statement, Seoul's joint chiefs of staff said the projectiles were launched towards the North's eastern waters after lifting off from the country's northeastern South Hamgyong province.
South Korea's military is monitoring possible further launches, but gave no further details, such as what kind of projectiles they were and where they landed.
Japan's Prime Minister Shinzo Abe has said Tokyo would be in close contact with its partners to keep a close eye on developments.
He said: "Multiple missile launches by North Korea are a serious challenge not only for Japan, but also international society.
"We will remain in close contact with the United States, South Korea and the international community to monitor the situation.
"We will increase our vigilance to preserve the safety and assets of the Japanese people.
Previously, such reports by the North and South have usually turned out to be test launches of missiles, artillery pieces and other weapons.
At the end of October, Pyongyang conducted what it called a test-firing of a new "super-large" multiple rocket launcher, a day after South Korea's military said the North fired two projectiles into its eastern waters.
On Monday, North Korea said its leader, Kim Jong Un, visited a tiny island and ordered artillery troops there to practice firing near the sea boundary, where several bloody naval clashes between the Koreas have taken place in the past.
South Korea immediately protested against the drills, saying they violated an agreement last year aimed at reducing military animosity.
North Korea has been stepping up pressure on the US to meet its end-of-year deadline to offer a new initiative to break their deadlocked nuclear diplomacy efforts.
Some experts say the North may resume testing long-range missiles and nuclear devices if the US fails to meet the deadline.
Negotiations broke down in February when President Donald Trump rejected Kim Jong Un's demands for major sanctions relief in return for partial disarmament.