The national observance began at 2:46 p.m., a year after a magnitude 9.0 earthquake set off a sequence of two other deadly disasters the country is still working to overcome, The Yomiuri Shimbun reported.
Solemn observances were held throughout the country in memory of almost 16,000 people killed in the earthquake, the ensuing tsunami and atomic meltdown at the Fukushima nuclear power plant.
Trains stopped running in Tokyo for a minute's remembrance and sirens were sounded throughout the country, The Washington Post reported.
The government says there are still 3,282 people missing and more than 330,000 others are living in temporary accommodations since the disaster.
The National Police Agency said almost 300,000 buildings were destroyed and at least 1 million other structures were damaged by the earthquake, tsunami or fires that followed.