The test, scheduled well in advance, was done from the USS John Paul Jones and comes a day after North Korea fired a ballistic missile over Japan.
The test, using Standard Missile-6 guided missiles, intercepted a medium-range ballistic missile target.
North Korea said its missile launch was to counter US and South Korean military drills, and was a first step in military action in the Pacific to “contain” the US territory of Guam. The launch was condemned by the United Nations as an “outrageous” act.
The MDA said the test gives the naval component of the missile defence system higher ability to intercept ballistic missiles in their terminal phase.
Japan has been worried that the United States has so far declined to arm it with powerful new radar, Reuters reported on Wednesday.
Japan is seeking a land-based version of the Aegis ballistic missile defence system, operational by 2023, as a new layer of defence to help counter North Korea’s missile advances.