A ministry official said the North had fired what was believed to be a Musudan missile at around 6:40 a.m (0310 IST) from Wonsan on the east coast, but it plunged back to earth seconds after launch.
"It is believed to have failed," the official said.
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North Korea initially tried to test a Musudan on April 15 -- the birthday of founding leader Kim Il-Sung -- but the exercise ended in what the Pentagon described as "fiery, catastrophic" failure, with the missile apparently exploding just after take-off.
The failed tests come as the country is gearing up for a rare and much-hyped ruling party congress next month, at which Kim Jong-un is expected to take credit for pushing the country's nuclear weapons programme to new heights.
There is growing concern that Pyongyang is preparing to conduct a fifth nuclear test in the run-up to the event which opens May 6.
Pyongyang has hailed a series of achievements in recent months, including miniaturising a nuclear warhead to fit on a missile, developing a warhead that can withstand atmospheric re-entry and building a solid-fuel missile engine.
Last Saturday, it successfully tested a submarine-launched ballistic missile (SLBM) and was sharply criticised by the UN Security Council.
Existing UN resolutions forbid North Korea from the use of any ballistic missile-related technology.
The Musudan is believed to have an estimated range of anywhere between 2,500 and 4,000 kilometres. The lower range covers the whole of South Korea and Japan, while the upper range would include US military bases on Guam.
The missile has never been successfully flight-tested.
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