Japan on Saturday marked the 20th anniversary of the Kobe earthquake that killed more than 6,400 people with renewed calls for the quake-prone nation to stay vigilant against the next "Big One."

More than 14,000 people gathered to commemorate the victims in the western port city of Kobe, where a 7.2-magnitude quake hit at 5:46 am on January 17, 1995.

The quake, which killed 6,434 people, levelled much of the city and sparked a major review of quake preparedness in the island-nation that suffers about one fifth of the world's most powerful tremors.

The warning was brought into reality four years ago when a 9.0 magnitude quake struck in March 2011, triggering a huge tsunami that smashed into the country's northeast coast, killing around 18,000 people and creating the world's worst nuclear emergency in a generation.

Kobe survivors and family members of victims gathered before dawn to lay bouquets and light thousands of candles in a park used as an evacuation centre after the 1995 jolt.

Later in the day, Emperor Akihito and Empress Michiko attended a memorial ceremony in the city and offered a one-minute prayer with some 500 other participants.

"By learning lessons from the disaster we will do our best to build a community

where we can live in safety," Eriko Yamatani, state minister for disaster management, told the ceremony.

The quake buried residents in flattened buildings and uprooted highway overpasses and train tracks, while fires raged through collapsed timber houses and acrid smoke darkened the sky.

Heavy damage to the harbour area, where nearly all of the 300 shipping berths were destroyed, dealt a severe blow to the city's economy, sparking a population exodus over the following months and years.

Japanese broadcasters and newspapers reminded citizens of the high probability of another big quake, with geologists saying a major event is overdue.

"We want to speed up preparations for building a strong country against disasters," the Asahi Shimbun said in an editorial.

"We cannot eliminate damage completely, but we can start making efforts any day now to reduce damage," the daily said.