Onodera said the ministry left the cruise missiles out of its initial funding request in August because it had not yet finalized arrangements with the developers.
The fiscal 2017 supplementary budget, expected to receive cabinet approval this month, will include money to introduce the Patriot Advanced Capability Missile Segment Enhancement, which doubles the protective range of the PAC-3 surface-to-air interceptors, as well as the FPS-7 long-range search radar.
It also plans to buy Joint Strike Missiles with a range of some 500 kilometres from Norway's Kongsberg Defence and Aerospace, news reports said.
The move is likely to be controversial, as Japan limits its military to self-defence.
But Onodera insisted his ministry will continue to uphold the policy, telling reporters: "We will introduce them as standoff missiles that allow us to deal with our opponents from outside the range of threats".
US President Donald Trump had caused consternation during his White House campaign by suggesting allies such as Japan need to do more to defend themselves, although since taking office Trump and his diplomats have offered reassurances of support.
Defense Minister Itsunori Onodera did not refer to North Korea when announcing the planned acquisition and said the new missiles would be for defense, with Japan still relying on the United States to strike any enemy bases.
Earlier this year North Korea tested missiles that hit the Sea of Japan just inside Japan's exclusive economic zone.
The call, however, has fallen short of persuading key North Korean backers China and Russian Federation to take steps to isolate the regime.