Remembrance ceremonies were held in towns and cities around the disaster zone and in Tokyo, where Emperor Akihito and Empress Michiko led tributes to those who died in Japan's worst peace-time disaster.
Television footage showed victims and volunteers joining their hands in prayer near the shell of a tsunami-hit building in the northeastern port town of Minamisanriku, one of the many stark reminders of the destruction.
Its gigantic force unleashed a towering wall of water that travelled at the speed of a jet plane to the coast. Within minutes, communities were turned to matchwood, and whole families drowned.
"The situation surrounding disaster victims remains severe," the emperor told the ceremony.
"It is important to continue making efforts to build a safer land without forgetting this lesson."
The National Police Agency said a total of 15,891 people are confirmed to have died in the disaster, with another 2,584 still listed as missing. Human remains are still occasionally found.
"Somebody needs to do this, walking along the shore," said Takayuki Ueno, who at the weekend combed a desolate winter beach for the bones of his three-year-old son.
In Shichigahama, 28 police and coastguard officers offered a silent prayer Wednesday morning before they began their search for the bodies of two townspeople still missing.
"We have found bones on the beach but they are mostly from animals," said Hidenori Kasahara, a police officer who was sifting through the sand.
The nuclear disaster that the tsunami caused at the Fukushima plant continues to haunt Japan and colour national debate.
The crippled plant remains volatile and the complicated decommissioning process is expected to last for decades.
Although there is little evidence so far, fears persist over the effect on health of radioactive leaks.
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