Japan is marking the first anniversary of the massive earthquake and tsunami that claimed nearly 16,000 lives.

With a moment of silence, prayers and anti-nuclear rallies, Japan marked one year since an earthquake and tsunami killed thousands and set off a radiation crisis that shattered public trust in atomic power and the nation's leaders.

Japan tsunami - then and now | Rebuilding shattered lives

A year after the magnitude 9.0 earthquake unleashed a wall of water that hit Japan's northeast coast, killing nearly 16,000 and leaving nearly 3,300 unaccounted for, the country is still grappling with the human, economic and political costs.

In the port of Ofunato, hundreds of black-clad residents gathered at the town hall to lay white chrysanthemums at an altar dedicated to the town's 420 dead and missing.

Just a kilometre from Tokyo Electric Power Company's (Tepco) wrecked Fukushima plant, where reactor meltdowns triggered the world's worst nuclear crisis since Chernobyl, residents of the abandoned town of Okuma were allowed back for a few hours to honour the dead.

Authorities have imposed a 20km no-go zone around the plant and residents may never be allowed back.

Along the northeast coast, police and coastguard officers, urged on by families of the missing, still search rivers and shores for remains even though the chances of finding any appear very slim.

The nation observed a moment of silence at 2.46pm (5.46am Irish time) when the quake struck.

The Japanese people earned the world's admiration for their composure, discipline and resilience in the face of the disaster while its companies impressed with the speed with which they bounced back.

As a result, the $5 trillion economy looks set to return to pre-disaster levels in coming months with the help of about $230 billion earmarked for a decade-long rebuilding effort agreed in rare cooperation between the ruling and opposition parties.

Yet people are increasingly disillusioned about the political establishment's ability to tell the truth and rise to the occasion, a deep lack of trust that one commentator called "the fourth disaster of March 11."

Politicians and bureaucrats drew fire for the chaotic response to the Fukushima disaster and their failure to seize the moment and tackle a myriad of ills that have dogged Japan for over two decades.

Anti-nuclear demonstrations in Tokyo and elsewhere also served as a reminder that many want bolder action than the government's preferred scenario of a gradual reduction in reliance on nuclear power.

Tepco, criticised by many for its failure to prepare for the disaster and its response to it, issued a fresh apology to mark the anniversary.

"We deeply apologise to residents near the Fukushima Daiichi plant, the people of Fukushima and wider society for the grave troubles and worries caused by the incident," Tepco President Toshio Nishizawa said in a statement.

Slow progress in drawing up plans for the tsunami-damaged and radiation-contaminated region is deepening the misery of survivors, about 326,000 of whom are still homeless, including 80,000 evacuated from the vicinity of the Fukushima plant.

While the government declared its reactors had reached "cold shutdown" in December, the country lives under a cloud of anxiety over the long-term health effects of radiation.

The plant's dismantling and the clean-up of an area the size of Luxembourg will take decades at an incalculable cost using technologies yet to be developed.

Taxpayers, facing proposed sales tax increases to help fund the country's debt, will need to cough up tens of billions of dollars to prop up the still politically powerful Tepco.