The South Korean military's joint chiefs of staff announced the launches from the southeast of the country -- the seventh and eighth in two weeks -- without giving further details.
"While strengthening our monitoring and vigilance, our military is maintaining a full readiness posture in close cooperation with the United States," the joint chiefs of staff said, Yonhap reported.
North Korea on Saturday had defended its recent flurry of missile tests as a legitimate counter to US military threats, following days of joint military exercises between the South, Japan and the United States.
The Japanese prime minister's office also confirmed at least one of Sunday's launches on Twitter.
"North Korea has launched a suspected ballistic missile. More updates to follow," the office said.
The missiles, fired toward the East Sea, also known as the Sea of Japan, seem to have fallen outside Japan's exclusive economic zone, the Japanese government said, according to Kyodo news agency. The coast guard said it had so far not received any reports of damage to Japanese ships, national broadcaster NHK reported.
Sunday's launches were the latest in a flurry that included an intermediate-range ballistic missile fired Tuesday over Japan, prompting an alert for people in affected areas underneath to take cover.
And on Thursday, North Korea fired two ballistic missiles, the same day Seoul, Tokyo and Washington carried out fresh exercises involving a US navy destroyer from the USS Ronald Reagan aircraft carrier's strike group.
The United States redeployed the nuclear-powered aircraft carrier to waters east of South Korea as part of a broad-ranging military response to Pyongyang's Tuesday test, which also included joint bombing and missile drills.
The carrier's redeployment prompted an angry response from the North, with the foreign ministry saying it posed "a serious threat to the stability of the situation on the Korean peninsula".
Exercises between South Korea and the United States concluded Saturday, according to Yonhap.
Seoul's military said it had scrambled 30 fighter jets Thursday after 12 North Korean warplanes staged a rare "formation flight north of the inter-Korean air boundary [and] conducted air-to-surface firing drills."
Thursday's launches seemed to be the first time North Korea had fired missiles from Samsok, near the capital.
The recent launches were "the just counteraction measures of the Korean People's Army", Pyongyang's foreign ministry said in a statement Thursday.
Also on Thursday, the United Nations Security Council held an emergency meeting to discuss Pyongyang's Tuesday launch over Japan.
At the meeting, North Korea's longtime ally and economic benefactor China blamed Washington for provoking the spate of launches by Kim Jong Un's regime.
US ambassador to the UN Linda Thomas-Greenfield called for "strengthening" existing sanctions on North Korea, something China and Russia vetoed in May.
Kim has declared isolated North Korea an "irreversible" nuclear power, effectively ending the possibility of denuclearisation talks.