The projectile reached an altitude, or apogee, of about 540 kilometres and travelled a distance of about 360km.
North Korea also fired two shorter-range missiles, including one that flew about 760km and reached an altitude of 60km, South Korea's Joint Chiefs of Staff said. All three were launched from an area near Pyongyang’s main airport.
The missile's flight was far shorter than its last test in March of an ICBM that reached an altitude of more than 6,200km and travelled 1,080km before splashing down in the sea west of Japan.
The Joint Chiefs said the North apparently lost the second missile 20km into flight while the third flew 760km on an apogee of 60km.
It also said the militaries of the US and South Korea had fired two surface-to-surface missiles in response to demonstrate the allies' striking capabilities.
Mr Biden wrapped up his first trip as president to South Korea and Japan on Tuesday, where he held discussions with the two US allies that host the bulk of American troops in the region.
He agreed with his South Korean counterpart Yoon Suk-yeol to start talks on expanding joint military exercises aimed at countering the threat posed by North Korea.
South Korean presidential representative Kang In-sun strongly condemned the launches, describing them as “illegal acts” and a “major provocation that threatens peace on the Korean Peninsula” and within the international community.
Japanese Defence Minister Nobuo Kishi called the launches unacceptable. He had said earlier that officials were looking at whether one of the rockets was an ICBM.
The US also condemned North Korea actions and called on Pyongyang to “refrain from further provocations” and choose dialogue.
A US State Department representative said the launches were in breach of several UN Security Council resolutions and were “a threat to the region”.
The country is barred from ballistic missile launches by the Security Council.
US national security adviser Jake Sullivan also condemned the launches in a phone call with his South Korean counterpart, Kim Sung-han, moments after returning to Washington with Mr Biden.
They both condemned Pyongyang's “destabilising ballistic missile tests and committed to continue building on their close co-ordination”, the White House said.
There was no indication on what type of ICBM North Korea fired on Wednesday. However, the White House said there were three missile launches, in line with an assessment by Seoul, which suspects that one was an ICBM.
North Korean leader Kim Jong-un has ignored US appeals to return to the negotiating table and his regime has yet to comment on what type of missile it fired.
South Korea said its neighbour launched its biggest and newest ICBM — a Hwasong-17 — on March 16 but it blew up in the skies over Pyongyang shortly after take-off.
Eight days later, it successfully launched a Hwasong-15 missile, which was last tested in 2017, Seoul said.
Agencies contributed to this report.