Residents huddled in an amusement park basement and a subway station while others ducked and covered their heads at a community center.
North Korea has twice launched ballistic missiles over northern Japan and test-launched intercontinental ballistic missiles in trajectories that fell inside Japanese exclusive economic waters.
At the Tokyo Dome City Attractions amusement park, an announcement over the intercom said that a missile was seen to have been fired. After North Korea's repeated missile launches, similar drills were held in other parts of the country, including Akita, Niigata and Toyama prefectures.
Less than a week before Monday's drill, Japanese public broadcaster NHK issued a false warning of an incoming missile that rattled nerves in the country.
North Korea last test-fired a missile on November 29 and has since restarted talks with South Korea, but Japanese Prime Minister Shinzo Abe appeared unimpressed by the latest developments, supporting the need for Japan to bolster its anti-missile defenses amid "the most severe security environment in the postwar era", as he described it in his speech to parliament on Monday, quoted in the Nikkei Asian Review.
North Korea launched two ballistic missiles over northern Japan at least twice a year ago, and test-fired another missiles in loft-trajectory into Japanese waters.
The drill was organized by the Tokyo Metropolitan and central governments in response to North Korea's repeated missile launches.
Meanwhile, park employees quickly ushered residents into reinforced concrete buildings and subway stations, shouting "a missile was launched, a missile was launched!"
Japanese Prime Minister Shinzo Abe offered his "100 per cent" backing to Donald Trump in the escalating tensions between the USA and North Korea last October ahead of the President's visit to Tokyo the following month. "So drills should be held repeatedly".
North Korea has singled out Japan, a key U.S. ally in the region, for verbal attacks, threatening to "sink" the country into the sea and to turn it into "ashes". Japan has also announced massive new purchases of military equipment, primarily from the United States.Speaking to CNN, Protester Tomoko Ito described the drills as "a practice for war".
But the 50-year-old said the drill would not be much use in the event of an actual attack.
"If there had been no guidance from the staff members, I think I would have been confused".