The Joint Chiefs of Staff said the launches happened from North Korea's capital region about 5pm on Thursday.
The military said the missiles were launched towards North Korea's eastern waters.
The military said South Korea has bolstered its surveillance posture and was closely co-ordinating information on the launches with the US and Japan.
South Korea's presidential national security council held an emergency meeting to discuss the launches.
After the meeting, the council issued a statement urging North Korea to halt ballistic missile launches that are banned by UN Security Council resolutions.
The Japanese prime minister's office had earlier said that it detected a suspected missile launch.
On Wednesday, the South Korean and US militaries said they were scaling back their 11-day Ulchi Freedom Shield exercises.
US President Donald Trump earlier ordered the Pentagon to "substantially reduce" the exercises, just before they began on Monday, citing what he said was a good relationship with Kim and South Korea's refusal to support him over the war in Iran.
Kim Yo-jong, the influential sister of North Korean leader Kim Jong-un, dismissed Trump's overture later on Wednesday.
She said it was not even worthy of comment.
"The provocative, aggressive nature of the drills won't change even though their duration and size were reduced," she said.
"If the US calculates that it can propagate its recent measure as the one of so-called good faith, they will not get the desired answer."
She also cited a series of other military drills carried out by the US and South Korea earlier in 2026 and South Korea's push to introduce nuclear-powered submarines.
Kim Yo-jong still refrained from the typical North Korean reaction of fiery rhetoric and said personal relations between her brother and Trump are "still excellent".
That signals North Korea would want to wait for Trump to make bigger concessions before returning to talks.
She denied Trump's claim that Kim Jong-un had responded to his request for a conversation.
When asked by reporters Wednesday if he would be meeting with Kim Jong-un in 2026, Trump said, "Yeah, I will be."
He would not answer a question about whether he was exchanging letters with Kim but said he got along with him.
