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.
"The military is keeping a tight surveillance over the North to cope with further provocations", the ministry added.
One appeared to have blown up nearly immediately while two flew about 250 km (155 miles) in a northeasterly direction, Pacific Command said, revising an earlier assessment that two of the missiles had failed in flight.
This latest North Korean missile test would be the 12th ballistic missile test this year.
The second missile appeared to have blown up nearly immediately at launch, the command said.
North Korea fired several short-range missiles into the sea off its east coast early on Saturday, South Korea and the USA military said, as the two allies conducted annual joint military drills that the North denounces as preparation for war, APA reports quoting Reuters. Early reports suggested that the missiles traveled only 150 miles before falling in the sea. The launches occurred in the midst of the US and South Korea's annual military exercises.
Six Army columns deployed in Panchkula post conviction of Ram Rahim verdict
Mobile internet services and data services have been suspended in Haryana , Punjab and Chandigarh for the next the 72 hours. Dera Sacha Sauda chief Gurmeet Ram Rahim had yesterday night released a video and asked his followers to abide by the law.
Since firing an intercontinental ballistic weapon last month, Pyongyang has threatened to aim missiles at the US Pacific territory of Guam.
Also on Tuesday, Secretary of State Rex Tillerson praised Pyongyang for demonstrating "some level of restraint", noting that there had been "no missile launches or provocative acts on the part of North Korea", since the United Nations Security Council voted August 5 to impose a $1 billion sanctions package against the country. The US ban on American citizens traveling to North Korea takes effect September 1.
On April 2009, Pyongyang launched a long-range rocket, which flew over Japan in what it said was an attempt to put a satellite into orbit, but which was seen by the US, Japan and South Korea as a disguised test of a Taepodong-2.
It is also believed to be developing a solid-fuel missile that could be used for submarine launches.
The North's move was immediately reported to President Moon Jae-in.