TOKYO—Japan said Thursday that it would reopen its border to a limited number of overseas students, workers and business travelers after a three-month ban that left scars on the country’s relations with foreigners.

The ban has been popular among voters and helped Prime Minister Fumio Kishida maintain healthy poll ratings during an Omicron infection wave. Opponents included Japanese business leaders and foreign students, who said the severe steps harked back to the country’s centuries of isolation from the 1600s through the...

TOKYO—Japan said Thursday that it would reopen its border to a limited number of overseas students, workers and business travelers after a three-month ban that left scars on the country’s relations with foreigners.

The ban has been popular among voters and helped Prime Minister Fumio Kishida maintain healthy poll ratings during an Omicron infection wave. Opponents included Japanese business leaders and foreign students, who said the severe steps harked back to the country’s centuries of isolation from the 1600s through the 1850s.

Héloïse Le Net has been waiting for 1½ years at her apartment in Paris for approval to enter Japan to study at a Tokyo language school. She visited Japan for the first time in 2019 with a friend instead of going to China, where the paperwork for tourists was cumbersome.

“I did not know Japan very well then, but I fell in love,” said Ms. Le Net, a 24-year-old contemporary dancer. “People were so nice.”

Héloïse Le Net of France in Kyoto during her first visit to Japan.

Photo: Héloïse Le Net

The warmth she felt then has dissipated. “The government is hard on gaijin,” or foreigners, she said as tears welled up in her eyes during a video interview. “We’re not welcomed.”

The ban took effect on Nov. 30 and prevented almost all foreigners from newly entering the country. Even before that, it had been difficult since early in the pandemic for people to go to Japan for work or study. Foreigners who already have residence permits have been permitted to re-enter.

Under the plan released Thursday, Japan will in principle allow non-Japanese workers, students and business travelers to enter the country starting March 1. The quarantine for arrivals will be reduced to three days or eliminated in certain cases.

Tourists remain banned, and the government is keeping a cap of 5,000 on the total number of daily entrants, both Japanese and foreigners. That is more than the current cap of 3,500 but a fraction of those waiting.

The immigration agency says that more than 400,000 foreigners have preliminary approval to reside in Japan and haven’t been able to enter.

Yohann Barraillé, 23, of France was supposed to go to Japan in September 2020 as an exchange student. He came to love Japanese manga such as Naruto and One Piece as a teenager and has studied the language for four years in Toulouse.

“We need to study Japan in Japan,” he said. “I’m ready to come. I’m ready to quarantine.”

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The Omicron wave in Japan, with as many as 100,000 daily cases recently, has reduced the benefit of keeping out a relative handful of foreigners who might be infected. Other countries have scaled back restrictions.

The U.K. has eliminated post-arrival testing if travelers are vaccinated. Rules for entering the U.S. are generally similar to before the pandemic except that travelers must show a negative coronavirus test or proof of recent recovery from Covid-19.

Japan’s months of isolation have exposed a gap between public opinion and business leaders. A poll conducted Feb. 11-13 by public broadcaster NHK found that 57% of respondents wanted to keep the border closed.

Sumitomo Chemical Co. Chairman Masakazu Tokura, who heads the nation’s largest business lobby, said Japan’s attractiveness as a place to do business might wane if travel curbs continued and people from other countries felt unwelcome. “I fear this could harm the national interest,” he said this month.

Marcus Schürmann, head of the German Chamber of Commerce and Industry in Japan, said some German companies were moving regional hubs to other countries in Asia. He said it would be “very, very hard to recover” from the damage.

Mr. Kishida, the Japanese prime minister, on Thursday defended the policy as necessary to limit infections and protect the public while more was learned about Omicron. He said that even with the loosening, Japan would have the strictest border policy among the Group of Seven industrialized nations.

“I hope people will understand that Japan is adopting a cautious response based on our society’s values emphasizing protection of the elderly and the weak,” Mr. Kishida said at the online World Economic Forum in January.

Ryosuke Nishida, a sociologist at Tokyo Institute of Technology, said the entry ban left a chilly impression on foreigners. “When it opens back up, will they choose Japan again?” he said. “It won’t be that simple.”

Japan, the most aged nation among developed countries, is likely to need some 6.7 million foreign workers in 2040, quadruple the current level, according to a study released this month by a unit of the government-owned Development Bank of Japan.

Ms. Le Net in Paris said a few friends who had wanted to study in Japan have switched to South Korea. But she isn’t giving up, she said, because she has been waiting so long and “I’m close to my goal.”

Write to Miho Inada at miho.inada@wsj.com