Today, these towns, economically depressed and with declining populations, are struggling to rebuild and recover. About 180,000 people remain displaced, with more than a third of them living in temporary housing.
At an official service at the National Theater in Tokyo on Friday, Prime Minister Shinzo Abe and Emperor Akihito remembered the dead.
"Whenever I go to disaster-hit areas, I find [damage of] the disaster still continues. Still, recovery has made certain progress even though one step is small," Abe, wearing a black tie, said.
The emperor said his "heart aches" when he thinks of those who still haven’t been able to return home.
"It’s important that Japanese people put their hearts as one and be considerate [for victims] in order not to leave anyone in difficulty behind, and let them go back to their ordinary lives as soon as possible," he said.
Memorial services, lantern-lighting ceremonies and candlelight vigils were held in Iwate, Miyagi and Fukushima prefectures, the worst hit by the disaster.
Around Tokyo, there were memorial ceremonies organized by Buddhist and Catholic groups, and an anti-nuclear “Peace on Earth” event at a park in the middle of the capital. People bowed their heads and closed their eyes for a moment's silence as bells and sirens rang out. Flags flew at half-staff.
The coverage in the Japanese media has been tear-jerking.
NHK, the state broadcaster, aired a documentary about a phone booth in Otsuchi, Iwate prefecture, that has been turned into a memorial spot. People can make a "call" to their dead relatives from “the phone of the wind,” or write a message in a notebook there.
It featured an old man saying into the phone: "Show up yourself fast. Come back fast ... wherever you are, I hope you are alive." A young man said: "If my voice can reach you, please listen to what I have to say...."
As part of its anniversary coverage, the Asahi Shimbun ran a story about the difficulties children in the tsunami-hit zone have encountered over the past five years.
“I do not like to see my mom’s picture because it saddens me,” Sora Sasaki, now 11 years old, told the newspaper. His mother, Kanako, died in the disaster at age 33.