Throngs nationwide observed a moment of silence at 2:46 p.m. local time (12:46 a.m. ET), the exact time the earth shook on March 11, 2011.
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"A lot of lives were lost ... I feel the grieving families' pain and I cannot express my sorrow enough," Prime Minister Yoshihiko Noda said at the ceremony.
Emperor Akihito, who is recovering from recent surgery, also attended.
"I'd like to express my mourning for the people who passed away a year ago ... almost 20,000 died and others remain missing. Many of them were firefighters," the emperor said.
Government officials and victims' relatives laid flowers at a shrine set up at the front of the theater.
In tsunami-ravaged towns along the northeast, residents solemnly placed wreaths where homes once stood. Warning sirens wailed in some areas at the precise time the quake struck.
Clad in black, residents of Ofunato gathered to pay tribute to hundreds of the town's residents killed during the earthquake and tsunami. Some wept quietly.
The 9.0-magnitude quake shifted the earth's axis and unleashed a wall of water that swept away lives and homes. Million of people fled for higher ground. Nearly 16,000 people died and 3,000 others remain missing. For those who survived that day, life is not the same.
"On the surface, it is business as usual," said Nicky Washida, a British expatriate who's lived in Japan for 10 years. "We wake up, we go to work, we shop for dinner. We drink, we laugh, we care for our children. But running underneath the veneer of normality is the constant reminder that life has changed."
Washida said something as simple as buying food has changed in the wake of the nuclear crisis. She said she reads labels to ensure there are no chances of contamination.
As residents scramble to return to normalcy, Noda recently addressed rebuilding efforts, which represent Japan's greatest challenge since the end of World War II.
"The Japanese people are united in working with the government to put all our might toward working on the reconstruction," Noda said this month. "The debris cleanup, the building of temporary houses and daily support for the disaster victims -- we have been making steady progress on all those issues," he said.
Following the quake and tsunami, Japan found itself dealing with the worst nuclear crisis since the 1986 Chernobyl disaster.
The Fukushima Daiichi nuclear facility was knocked offline, resulting in a meltdown of three reactors, with radiation leaking into the air and contaminated water spilling into the sea. While no deaths were attributed to the nuclear disaster, more than 100,000 people remain displaced from the towns where its long-lived fallout settled.
"While always keeping in mind the tremendous responsibility we have to maintain stable conditions at Fukushima Daiichi nuclear plant, we will continue to safely work toward the mid-to-long term decommissioning of the reactors," said Tokyo Electric Power Co., which owns the plant. "In addition, all TEPCO group companies will further intensify their efforts to care for the presently afflicted and provide the compensation due them in a swift manner."
One year on, Japan is far from dug out of the destruction wrought by the triple disaster, but the prime minister said he is committed to rebuilding and in re-energizing the nation in the process.
For some of the nation's youth, hope reigns amid the heartbreak and ruins.
"A lot of Japanese are very optimistic, so don't worry about (us) too much," said Kohei Maeda.