Emperor Akihito, Empress Michiko, Prime Minister Shinzo Abe and other participants at a national ceremony in Tokyo bowed their heads along with residents across the affected region at 2:46 pm (1116 IST) - the exact moment on March 11, 2011 the magnitude 9.0 quake struck under the Pacific Ocean.
The massive earthquake unleashed a giant wall of water that swallowed schools and entire neighbourhoods, with unforgettable images of panicked residents fleeing to higher ground and vehicles and ships bobbing in the swirling waters of flooded towns.
In the northern city of Sendai in Miyagi prefecture -- the region that suffered the most deaths -- survivors and bereaved family members gathered at a Buddhist statue built for the repose of victims' souls in front of a huge breakwater at Arahama beach where massive waves came ashore five years ago.
Some joined hands in prayer, while a woman threw a bouquet of flowers into the sea.
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Police and firefighters were seen combing that beach and others in continuing efforts to find evidence of victims, including bones, as many families say they still cannot abandon hope of seeing their loved ones again.
"I feel pain in my heart when I think of people who still could not return home," he said.
Some areas remain uninhabitable, though in others residents have been cleared to return.
The situation remains fragile in Fukushima prefecture, where the nuclear plant suffered explosions that spread radioactive material into the surrounding countryside and ocean. The crisis forced tens of thousands of nearby residents to flee their homes, farms and fishing boats.
Tokyo Electric Power, the operator of the shuttered plant, admits it has only made small steps in what is likely to be a four-decade battle to decommission the crippled reactors.
Despite public opposition to nuclear power as a result of the disaster, the government has pushed to restart idled reactors, saying they are essential to power the world's third largest economy.