Japan’s Prime Minister Fumio Kishida delivers a speech in Tokyo, Japan. File/Reuters

Japan said on Monday it would close its borders to foreigners, as the world's third-largest economy joined Israel in taking the toughest measures against the new coronavirus variant Omicron, which also cast a cloud over Australia's re-opening plans.

Japan would bar entry to foreigners from midnight on Monday in account of the spread of the Omicron variant of coronavirus variant's discovery in South Africa, and Japanese returnees from a number of specified nations would have to quarantine in designated facilities, Prime Minister Fumio Kishida told reporters.

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"These are temporary, exceptional measures that we are taking for safety's sake until there is clearer information about the Omicron variant," Kishida told reporters.

"I'm prepared to bear all criticism from those saying the Kishida administration is being too cautious."

A medical worker carries RT-PCR swab tests outside the international terminal at Sydney Airport. Reuters

It could take "days to several weeks" to understand the level of severity of the variant, says the World Health Organisation (WHO), which flagged Omicron as a "variant of concern".

As a precaution to avert a worst-case scenario, Japan will close its borders to all foreigners from midnight on Tuesday, Prime Minister Fumio Kishida said.

"Japan will first of all ban the entry of foreigners," he told reporters, adding that Japanese returning from specified nations would face quarantine in designated facilities.