US and South Korean forces had been on heightened alert for a medium-range ballistic missile test in recent weeks amid tensions triggered by North Korea's nuclear test in February.
"North Korea launched two guided missiles in the morning and another one in the afternoon," a defence ministry spokesman told AFP.
"The missiles landed in the East Sea (Sea of Japan)," he said.
South Korea was maintaining intense surveillance of the North and keeping a high-level of readiness to deal with any risky developments, he added.
North Korea sometimes launches short-range missiles for tests or as part of military drills.
"A more detailed analysis will be needed but the missiles launched may be a modified anti-ship missile or the KN-02 surface-to-surface missile derived from the Soviet era SS-21 that has a range of about 120 kilometres," a Seoul official told Yonhap news agency.
Following the move, the US urged the North to exercise restraint, without specifically commenting on the launches.
"We are closely monitoring the situation on the Korean Peninsula. As is standard practice, we do not comment on intelligence matters," Darby Holladay, a State Department spokesman said.
"We continue to urge North Korea to exercise restraint and take steps to improve its relations with its neighbours." Seoul meanwhile branded the tests "serious" provocations.
"The international community will levy much tougher sanctions against North Korea for its continued absurd provocation," Min Hyun-Joo, spokeswoman of the ruling Saenuri Party, was quoted as saying by Yonhap.
"No compensations or benefits will be allowed if North Korea fails to show changes in its policy toward the right direction," she added.
The launches followed a joint South Korea-US naval exercise this week, slammed by North Korea as a "wanton" provocation and rehearsal for war.