The launch is the first by the North since it test-fired a missile on July 28 that could have been created to reach 10,000 km (6,200 miles), putting parts of the US mainland within reach.
One of the three missiles blew up "almost immediately", with none of the weapons posing a threat to either North America or the United States territory of Guam, the spokesman said.
The "unidentified projectiles", fired at 06:49 a.m. (21:49 GMT Friday), flew some 250 kilometres (155 miles) the ministry said.
South Korean President Moon Jae-in said in response to the launches: "The military is keeping a tight surveillance over the North to cope with further provocations". Nor, indeed, are they said to have done any damage.
The U.S. characterized them as short-range ballistic missiles.
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The United States has said that three short range ballistic missiles filed by North Korea on Saturday have failed.
Earlier this month Trump had warned that North Korea would be met with "fire and fury", if it continued with its threats.
The rival Koreas recently saw their always testy relationship get worse after Trump traded warlike threats.
The firings come after the United Nations agreed to impose costly economic sanctions on the country.
In recent weeks the North has threatened to fire a salvo of missiles toward Guam, but has since backed away from the plan and tensions have eased.
"The second missile launch at 12.07pm appears to have blown up nearly immediately".
Lee Il-Woo, an analyst at Korea Defence Network, said the launches represented a "low-level provocative act" carried out in response to the US-South Korea exercises, which are seen by Pyongyang as a rehearsal for an invasion of its own territory. -South Korea war games. Guam is a US island territory that is home to two American military bases. U.S. officials say none of the missiles posed any threat to North America at any point.
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