Hundreds of thousands of Japanese citizens have been advised to evacuate as waves of more than a metre hit coastal areas, public broadcaster NHK reported.
This was after the eruption of an underwater volcano off Tonga triggered tsunami warnings.
Around 230,000 people, most of them from areas hit by Japan's deadly 2011 tsunami, were advised to evacuate across eight prefectures due to the tsunami risk, NHK reported.
Ten boats were capsized in Kochi prefecture on Shikoku island in southern Japan, NHK said, and Japan Airlines cancelled 27 flights at airports across the country.
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The overnight disruption caused delays to rail and postal services in some areas, Kyodo News reported, with some residents passing a cold night after evacuating to higher ground.
A red tsunami warning - the second-highest in Japan's domestic scale - for Iwate prefecture in northern Japan was lifted late in the morning local time, NHK reported, with the less severe yellow tsunami advisory in place along Japan's eastern coast lifted at 2:00 pm (0500 GMT) local time.
Tsunami-hit Tonga remained largely uncontactable on Sunday with telephone and internet links severed, leaving relatives in faraway New Zealand praying for their families on the Pacific islands as casualty reports had yet to come through.
An underwater volcano off Tonga erupted on Saturday, triggering warnings of 1.2-metre tsunami waves and evacuation orders on the shores of Tonga as well as several South Pacific islands, where footage on social media showed waves crashing into coastal homes.
Internet and phone lines went down at about 6.40 p.m. local time on Saturday, leaving the 105,000 residents on the islands virtually uncontactable.
There are no official reports of injuries or deaths in Tonga as yet although communications are limited and contact has not been established with coastal areas beyond the capital Nuku'alofa, Jacinda Ardern the Prime Minister of New Zealand told a news conference on Sunday.
Tonga, an island nation with around 105,000 residents, lies 2,383 kilometres (1,481 miles) northeast of New Zealand.
"Nuku'alofa is covered in thick plumes of volcanic dust but otherwise conditions are calm and stable," Ardern said.
"We have not yet received news from other coastal areas," she said.
Satellite images captured the volcanic eruption on Saturday as the explosion sent plumes of smoke into the air and about 12 miles above sea level. The sky over Tonga was darkened by the ash.
Concerns were growing among the Tongan community in New Zealand, desperate to make contact with their families back home. Some churches organised community prayers in Auckland and other cities.
"We pray God will help our country at this sad moment. We hope everybody is safe," Maikeli Atiola, the Secretary of the Wesleyan Church of Tonga in Auckland said, Radio New Zealand reported.
Ardern said the main undersea communications cable has been impacted, likely due to loss of power.
Power was being restored in some areas on the islands and local mobile phones were slowly starting to work, she added.
Official damage assessments were not yet available, she said. But Ardern said the New Zealand high commission in Nuku'alofa had said the tsunami has damaged boats, shops and other infrastructure.
Tonga's cabinet held a crisis meeting on Sunday and was contacting development partners, a spokeswoman for Zed Seselja, Australia’s minister for international development and the Pacific told Reuters. She said Australia would have sent a P8 surveillance aircraft to Tonga on Monday.