The 9,200-ton USS Mustin, with a crew of 300 sailors and equipped with missile tracking and engaging systems, will be permanently deployed at Yokosuka, spokeswoman Hanako Tomizuka said on Saturday.
The Yokosuka facility in Tokyo Bay, home of the US Navy's Seventh Fleet, is the largest US Navy base in Japan.
A salvo of missile tests by North Korea this week, including the launch of a long-range Taepodong-2 missile, has unsettled the region and led to calls for the United Nations Security Council to impose international sanctions on Pyongyang.
North Korea has insisted that it has the right to test the missiles, and has said it will consider sanctions against it a declaration of war. Much of its anger has been aimed at Japan for pushing for sanctions.
Japan has also banned a North Korean ferry, the only regular direct link between the two countries, from entering its ports for six months as part of a package of initial sanctions.
A poll published on Saturday found that four-fifths of Japanese think their country should step up economic sanctions against North Korea in response to the missile launches.
A total of 80.7 per cent favoured stronger sanctions such as blocking money remittances to North Korea or curbing trade with Pyongyang, according to a survey of 1,011 people conducted on Friday and Saturday by Kyodo news service.
On North Korea's missile firings, 87 per cent expressed anxiety, with 45.2 per cent saying they "feel very anxious" and 41.8 per cent saying they "feel somewhat anxious", it said.