Much of the Tohoku coast hit by the disaster remains empty except for mounds of dirt brought in to raise the ground level to minimise risks from future tsunamis before any rebuilding is done.
Some areas remain no-go zones due to the high radiation.
"Give me back my hometown!" read a placard carried by an anti-nuclear demonstrator in front of the headquarters of plant operator Tokyo Electric Power Co on Thursday night. Others criticised Prime Minister Shinzo Abe and called for abandoning nuclear power altogether.
In coastal Rikuzentakata, which was flattened by a wave as much as 17m high and lost 7 per cent of its population along with its entire downtown, the pain remains strong.
"Infrastructure is recovering, hearts are not. I thought time would take care of things," said Eiki Kumagai, a volunteer fireman who lost 51 colleagues, many killed as they guided others to safety.
"I keep seeing the faces of those who died ... There's so much regret, I can't express it."
Abe and Emperor Akihito took part in a ceremony in Tokyo that included a moment of silence at the time of the quake, 2.46pm local time (6.46pm NZT), with bells ringing in the city centre as residents across the nation bowed their heads.
Japan, one of the world's most seismically active areas, marked the day with prayers and graveside visits. All the trains on the vast Tokyo underground network halted to mark the moment the quake struck.
Billions of dollars in government spending have helped stricken communities rise from the ruins, including elevating the earth to protect them from future waves and cleaning radiation-contaminated land, but much remains to be done for thousands still languishing in barracks-like temporary housing.
"I get the feeling that the number of people who don't know what to do, who aren't even trying, is increasing," said Kazuo Sato, a former fisherman from Rikuzentakata. "Their hearts are in pieces."
Government spending on reconstruction is set to dip from the start of the new fiscal year in April. But Abe pledged continued support.
"There are still many people living difficult lives in temporary housing and those who because of the nuclear accident cannot return to the places they lived," Abe told reporters on Thursday.
"We will speed up our efforts to build housing and disaster-proof towns ... so they can return as quickly as possible to permanent housing and stable lives," he said.
Abe pledged to bolster reconstruction efforts ahead of the 2020 Tokyo Olympic Games.
Force of nature
15,894 People killed by the tsunami and earthquake.
2561 People missing and presumed dead.
12 Prefectures affected out of a total of 47 in Japan.
$343.4b The budget earmarked for reconstruction for the first five years.
470,000 People evacuated in March 2011.
180,000 People who still have not returned home.
121,803 Houses destroyed.
64,988 People still in prefabricated temporary housing.
60 per cent Of planned public housing completed.
- AAP
