Timed to commemorate the anniversary of the Great Kanto Earthquake of 1923 which killed more than 100,000 people, the national Disaster Prevention Day has been held every year since 1960.
This year's drill saw the government simulate its response to a powerful earthquake in central to western Japan, a major natural disaster that researchers say may occur within 30 years or so.
The government estimates that a magnitude-9.1 temblor would kill over 320,000 people in the worst-case scenario.
A total of 1.33 million people are expected to participate in exercises during the day, Kyodo News agency said.
In central Shizuoka Prefecture, people participated in a drill based on a scenario that Mount Fuji, an active volcano, erupts following a massive quake, Jiji Press said.
On March 11, 2011, a 9.0 magnitude quake struck seismically-active Japan, triggering a massive tsunami that left over 18,000 dead or missing and sending reactors at the Fukushima nuclear plant into meltdown.