The Diet on Thursday enacted a law banning drones from flying over important facilities such as the Prime Minister's Office while giving police the power to destroy drones if necessary.
The legislation is expected to take effect before a foreign ministerial meeting of the Group of Seven industrial nations takes place in Hiroshima on April 11-12.
Prime Minister Shinzo Abe's ruling coalition had been seeking early enactment of the bill to strengthen anti-terrorism measures ahead of the G-7 summit in Mie Prefecture in late May.
The Civil Aeronautics Law was revised to regulate drone flights in September after a small drone was found on the roof of the building housing the Prime Minister's Office last April.
A man was later convicted over the incident. The drone carried a container filled with radioactive soil and the man's lawyers said he flew the drone onto the roof in protest over the government's nuclear policy.
But the amended law was seen as insufficient to deal with possible terrorist attacks using drones, as it failed to empower law enforcement authorities to destroy them if and when it was deemed necessary.
Key facilities over which drone flights will be banned include the Imperial Palace and facilities where important foreign dignitaries are staying.