Pyongyang is under a self-imposed blockade after closing its borders early last year to protect itself against the coronavirus pandemic.
The nuclear-armed North fired "two unidentified ballistic missiles" from its central inland area into the sea off its east coast, Seoul's joint chief of staff said in a statement.
"South Korean and US intelligence agencies are conducting detailed analysis," they added, without immediately giving details of the missiles' range.
The launch came as Chinese foreign minister Wang Yi is in Seoul for talks with his South Korean counterpart.
Speaking before the news emerged, Wang hoped that all countries would help "peace and stability on the Korean Peninsula", Yonhap news agency reported.
"For example, not only the North, but also other countries are engaging in military activities," he added.
"Having said this, we all have to work together toward the resumption of dialogue."
North Korea is under international sanctions for its nuclear weapons and ballistic missile programmes, which it says it needs to defend itself against a US invasion.
Talks with the United States have been stalled since the collapse of a 2019 summit in Hanoi between North Korean leader Kim Jong Un and then-president Donald Trump over sanctions relief -- and what Pyongyang would be willing to give up in return.
Kim has not visit China for more than six years after inheriting power from his father and predecessor Kim Jong Il, and tensions mounted in the allies' relationship.
But subsequently, he and Chinese President Xi Jinping met several times, and Beijing sees the North as very much part of its sphere of influence.
Yang Moo-jin, a professor at the University of North Korean Studies in Seoul, said Wednesday's launch "looks like North Korea's indirect message and even request to Beijing for the Korean peninsula to be addressed as a central agenda issue for China".
"At the same time, Pyongyang seems to be claiming and stressing that North Korea is taking the lead in the Korean peninsula issue," he added.
Wednesday's launches came days after the North's official Korean Central News Agency (KCNA) reported that it had test-fired a new "long-range cruise missile" over the weekend, calling it a "strategic weapon of great significance".
Pictures in the Rodong Sinmun newspaper on Monday showed a missile exiting one of five tubes on a launch vehicle in a ball of flame, and a missile in horizontal flight.
Such a weapon would represent a marked advance in North Korea's weapons technology, analysts said, better able to avoid defence systems to deliver a warhead across the South or Japan -- both of them US allies.
The missiles fired at the weekend travelled 1,500-kilometres (about 930 miles), on two-hour flight paths -- including figure-of-eight patterns -- above North Korea and its territorial waters to hit their targets, according to KCNA.
Pyongyang is not banned from developing cruise missiles, which it has tested previously.
The North's weapons programmes have made rapid progress under Kim, but it has not carried out a nuclear test or an intercontinental ballistic missile launch since 2017.
The US, Japanese and South Korean envoys on the North met in Tokyo earlier this week when Washington's representative Sung Kim re-iterated: "We hope that the DPRK will respond positively to our multiple offers to meet without preconditions."
The US was willing to "address areas of humanitarian concerns regardless of progress on denuclearisation", in keeping with international standards for access and monitoring, he added.