The Japan Metrological Agency has lifted the tsunami warning following the 6.9 magnitude earthquake that jolted off the coast of Japan.

Earlier, the agency issued a tsunami warning saying the waves could reach as high as three meters. Thousands were evacuated from the coastal areas while minor injuries were recorded among residents.

The tsunami "warning" was downgraded to "advisory" level but called on residents to prevent coastlines. Local residents were allowed to return to their homes after the lifting of the warning around early afternoon.

The Tokyo Electric Power Company (TEPCO) reported that the cooling system in one of the reactors at Fukushima Daini has stopped but there is enough water in the reactor to keep the fuel rods to operate in short period.

JMA also informed that the depth of the Tuesday's earthquake was 30km (18.6 miles). Residents in Tokyo experienced a strong tremor for 30 seconds.

Rupert Wingfield- Hayes, BBC's corresponded, reported that at least ten thousand people were evacuated and transferred to higher grounds.  Ships that are embarked at Fukushima were seen moving to move to safety place and the factory of Nissan has issued work suspension.

It may recall the 2011 disaster killed 16,000 people and 2,500 were missing as the sea water rose to 130 feet at Miyako in Iwate Prefecture. The government issued a lot of tsunami warnings in the prone area to evacuate. Sirens rang continuously in the coastal as the government take no chances to warned and evacuate the residents.

Japan lies in a seismically active region and has recorded to experienced 20 percent of 6.0 magnitudes or higher.