Japan has mourned the thousands who lost their lives in a massive earthquake and tsunami five years ago that turned towns to matchwood and triggered the world's worst nuclear disaster since Chernobyl in 1986.

The nine-magnitude quake struck offshore on a chilly Friday, sparking huge black waves along a vast swathe of coastline and killing nearly 20,000 people.

The tsunami crippled the Fukushima Dai-ichi nuclear plant, where meltdowns in three reactors spewed radiation over a wide area of the countryside, contaminating water, food and air.

Naoto Kan, the prime minister at the time, has said he feared he would have to evacuate the Japanese capital Tokyo and that Japan's very existence could have been in peril.

More than 160,000 people were evacuated from nearby towns and some 10 per cent still live in temporary housing. Some areas remain no-go zones due to high radiation.

Demonstrators in front of plant operator Tokyo Electric Power Co (Tepco) bore signs saying, "Give me back my hometown!"

At cemeteries along the devastated coastline, in front of buildings hollowed out by the wave, and on beaches, families gathered to offer flowers and incense, bowing their heads and wiping away tears.

Flags at central government buildings were at half-mast, some draped in black.

In coastal Rikuzentakata, which was flattened by a wave as much as 56ft high and lost seven per cent of its population along with its entire downtown, pain remains strong.

"The reality is that we still feel the scars here, and there are still many struggling to restart their lives," said 65-year-old Yashichi Yanashita, a retired city hall official. The four-storey town hall was inundated by the wave.