Two missiles were launched in the morning, followed by another in the afternoon, South Korean Defense Ministry spokesman Kim Min-seok told The New York Times.
“We remain vigilant and prepared in case the launching of these missiles might be followed by a military provocation by the North,” he said.
The launches followed a joint US-South Korea naval exercise this week.
Analysts said the missiles were likely fired in protest of those naval exercises and to draw attention from the international community, particularly the US.
The Musudan missiles have an estimated range of 1,500 to 2,500 miles, enough to reach South Korea and Japan and potentially US military bases on Guam.
The news comes after tensions appeared to have eased in the wake of a recent series of bellicose statements from Kim Jong-Un directed at the US and South Korea.
Earlier this year, North Korea threatened nuclear strikes on Seoul and Washington over joint US-South Korea military drills and UN sanctions imposed following its third nuclear test in February.
Both Koreas also pulled workers from a jointly-run factory complex after Pyongyang blocked inbound traffic earlier this year, with the final South Korean workers just now returning home.