The specialised unit will be set up within the Foreign Ministry next week, Chief Cabinet Secretary Yoshihide Suga said.
It will involve staff from the foreign and defence ministries, the National Police Agency and the Cabinet Intelligence and Research Office, Japan's current equivalent of the US CIA.
Intelligence-gathering staff will be sent to areas susceptible to terrorist activities, including parts of Southeast Asia, the Middle East and northwestern Africa, Suga said.
He cited a "severe safety situation" in the world. The push to improve anti-terrorism intelligence capabilities has gained urgency as Japan prepares to host a Group of Seven summit next year, and the Olympic Games in Tokyo in 2020.
"There is a growing need to gather intelligence that could affect Japan. Japan cannot remain unelated to any threat of terrorism, even if it's outside the country or not directly affecting us," he said.
About 20 experts will join the unit in Tokyo at the launch, while 20 others will be assigned to Japanese embassies and other overseas posts as intelligence officers, Ono said.
Until then, Japan seldom had been a target of such attacks. But concerns are rising as Japan, a top US ally, seeks a larger international military role under Prime Minister Shinzo Abe.
Ono said the intelligence-gathering staff will not be like those in spy movies.
"We do not plan any activity deemed illegal," he said.
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