The Tokyo police will introduce interceptor drones with nets to catch suspicious drones in sensitive areas.
The move would be a first in Japan, which tightened drone regulations after one was found on the roof of the prime minister's office in April carrying a small amount of sand contaminated with radiation.
The Metropolitan Police Department plans to launch the unit in charge of the interceptor drones this week, Jiji Press reported on Wednesday, citing an unnamed source.
The interceptors, dangling a rectangular net and equipped with a camera, will only be deployed against suspicious drones after attempts to locate and warn their operators.
The latest regulations ban drone flights near airports, in densely populated areas and anywhere more than 150 metres off the ground.
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Violators face a fine of up to 500,000 yen ($A5,550).
A former air force member was charged in May over the drone at the premier's office.
He said it was an act of protest against nuclear power.
The sand reportedly came from Fukushima prefecture, where a tsunami and earthquake in March 2011 cause meltdowns and explosions at a nuclear powerplant, and widespread contamination.
