Japan is also concerned with China's increasing naval activity in the waters surrounding its shores and is taking measures to bolster its coastal defenses, the report said.
The North Korean missile called the Musudan is based on Russian technology acquired in the 1990s and is designed for launch from mobile platforms, the ministry said in its 2011 white paper. Tuesday's report was the first time Japan has officially mentioned the missile by name.
According to the report, the missile would have an estimated range of 1,500-2,500 miles (2,500-4,000 kilometers). Guam is about 2,000 miles (3,200 kilometers) from North Korea.
That is less than the multi-stage Taepodong-2 missile, which is believed capable of reaching the U.S. west coast. But it would put the 50,000 U.S. troops based in Japan and thousands more on the island of Guam within its potential reach, the report said.
"Because of the secretive nature of the North Korean regime, it is extremely difficult to confirm its military intentions," the report said, adding that the North's mobile and underground missile facilities are believed to be intended to make early detection more difficult.
The report did not say when Japan expected the missile to be operational, or whether it already is.
Experts have long speculated that North Korea was working on a new intermediate-range missile. A missile believed to be a Musudan was displayed in a North Korean military parade last October.
Regarding China, Tokyo continues to be concerned by exercises held in the Pacific and in waters surrounding Japan, a concern it said has been heightened by what it called China's long-standing failure to provide data that would reassure the world of the peaceful intentions of its rapid military modernization.
Japan, the report said, is especially worried by the Chinese navy.
"China plans to expand its sphere of maritime activities, carrying out operations and training as an ordinary routine practice in waters surrounding Japan, including the East China Sea and the Pacific Ocean, as well as the South China Sea," it said.
Though it did not specifically link them to China, the report said Japan is boosting its submarine fleet while strengthening its troops and radar capabilities along its southwestern shores, which are closest to Taiwan and the sea lanes the Chinese navy has been more frequently using.