There were concerns North Korea might be preparing to test-launch missiles and conduct another underground nuclear test despite the severe international sanctions it is facing.
Chief Cabinet Secretary Yoshihide Suga said the Patriot Advance Capability-3 missile interceptor units were deployed at the Defense Ministry's headquarters in Ichigaya in Tokyo's Shinjuku Ward, the Ground Self-Defense Force's Camp Asaka in Tokyo's Nerima Ward and Camp Narashino in Funabashi in Chiba prefecture, the Japan Times reported.
The report said the units, with a range of about 30 kilometers (about 18.5 miles) , are designed both to defend the ministry's headquarters and key military units, as well as the heart of the capital. Suga gave no other details.
"We'd like to refrain from explaining further because it would give away details of the cards we hold. At any rate, we have taken thorough measures to ensure the safety of the people," Suga said.
The latest steps come in the wake of Japan's earlier deployment of Aegis destroyers, which are equipped with SM-3 interceptor missiles, in the Sea of Japan to monitor any launch of North Korean ballistic missiles.
North Korea, irate over the tightening of U.N. Security Council sanctions in response to its third nuclear test in February as well the U.S.-South Korea military drills, has issued a number of dangerous threats that have inflamed tensions on the Korean Peninsula and raised concern in the United States, South Korea and Japan.
The Japan Times said the Patriot PAC-3 units can intercept missiles that evaded the SM-3s on the Aegis destroyers.
Kyodo News quoted Prime Minister Shinzo Abe that his government would take all steps to protect Japanese lives.
On Sunday, Japanese Defense Minister Itsunori Onodera had ordered the country's military to be ready to shoot down North Korean missiles if they reach Japan, Kyodo said.
"There is not a high possibility that a missile would target Japan, but we have determined we should prepare for any contingency," a source told Kyodo.