The shows were held at secret locations, each lasting five minutes from 20:00 local time (12:00 BST).
Organisers set a time limit for the displays to avoid crowds gathering.
Initially, they said the time and date of the event would not be revealed but later reversed course, deciding a sudden pyrotechnics show could cause distress to some.
Filling the skies with a burst of light, the fireworks lasted long enough for people who did not know about it in advance to view them from the street or their homes.
Yet, the fireworks still drew modest crowds in places. In the capital Tokyo, people were seen watching the displays near the Tama River, before dispersing when they were over.
"I had a hunch, so I came here," one of the spectators, Yukiji Kushiro, told Japanese newspaper the Mainichi Shimbun. "Even though they say it's a secret, there are only so many places they can launch fireworks."
Dozens of firework-makers nationwide were involved in organising the synchronised displays, a project called "Cheer up Hanabi".