TOKYO—Life in Japan is showing tentative signs of returning to normal, but a fresh challenge may be facing the expatriates and Japanese who left and are now trickling back to their offices: how to cope with ostracism and anger from their colleagues who have worked through the crisis.

One foreigner, a fluent Japanese speaker at a large Japanese company, said that his Japanese manager and colleagues were "furious" with him for moving to Osaka for three days last week and that he felt he was going to have to be very careful to avoid being ostracized upon returning to work in Tokyo.

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The flight of the foreigners—known as gaijin in Japanese—has polarized some offices in Tokyo. Last week, departures from Japan reached a fever pitch after the U.S. Embassy unveiled a voluntary evacuation notice and sent in planes to ferry Americans to safe havens. In the exodus, a new term was coined for foreigners fleeing Japan: flyjin.

The expat employees' decision to leave is a sensitive cultural issue in a country known for its legions of "salarymen": loyal Japanese employees whose lives revolve around the office, who regularly work overtime and who have strong, emotional ties to their corporations and their colleagues.

"There is a split between [the Japanese and foreigners] on where their allegiances lie. In Japan, the company and family are almost one and the same, whereas foreigners place family first and company second," said Mark Pink, the founder of financial recruitment firm TopMoneyJobs.com, based in Tokyo.

The head of the Tokyo Stock Exchange, at a news conference Tuesday, expressed his disappointment that so many foreigners—from the U.S., France, the U.K., China and Hong Kong, among others—had been urged to leave the country by their governments and by worried families. Their flight was at least in part due to the more alarmist tones the foreign media took in coverage of the disaster, compared with the local news that emphasized how problems were being addressed.

"Many countries arranged for planes to bring their people back home. In some embassies, they sent messages to their nationals in Japan that the situation is very dangerous, while at some companies, top executives have come to Japan to provide reassurance," said Atsushi Saito, head of the TSE. "It may be part of TSE's role to put down rumors and to transmit to foreign nations what a great country Japan is."

One expat in Tokyo, who runs his own small business, decided to go to London last week with a business partner. "It has been the right thing to do from a work-productivity point of view, as we have a big deadline to meet at the end of the month," he said. "That said, I don't feel very good about leaving and I'm sure people will perceive it as cowardly, and I won't object to that."

Passengers, among them foreign nationals, checking in for flights departing from Narita International Airport, near Tokyo, on Sunday. European Pressphoto Agency

Those foreigners who return will find life in Tokyo is largely back to normal, with trains crowded during rush hour and men in suits packing restaurants during lunchtime in the city's main financial district. But signs of disruption linger: Many shops close at 6 p.m. to conserve electricity and many stores are still out of basics such as milk and toilet paper.

One foreign investment banker in Tokyo says he wasn't surprised that so many employees left. "We don't hire people into the financial industry to risk their lives—this is investment banking and we hire investment-banker types," he said. "We are trying to avoid ostracism for those who come back—there is no upside in that—but there is good-natured hazing."

To be sure, most foreign senior-level managers leading teams in Tokyo stayed in the capital or relocated their entire offices to other locations in Japan, according to several managers interviewed Tuesday. In most cases, the expats who left are stay-at-home mothers, their children and those workers who don't have staff reporting to them and can work remotely from Hong Kong and Singapore. Some Japanese, of course, also left Tokyo, though mainly women and children going home to their families in other parts of Japan, while their husbands stay in behind to work.

"If I had left as the president, my role as a leader would have been diminished," said Gerry Dorizas, the president of Volkswagen AG's operations in Japan, who has been in that role four years. "We've been very transparent."

VW Japan has moved all its staff, including 12 expats and 130 Japanese staff and their families, to Toyohashi in Aichi prefecture.

Boeing Co. , which has operated in Japan for more than 50 years, says the majority of its 30-strong staff in Tokyo have remained, despite an offer to work in Nagoya, or for expats to take a home leave.

Christine Wright, managing director of Hays in Tokyo, one of the country's leading recruitment firms, said: "I saw no reason to leave; if you have a commitment to your staff, you stay there."

Some said the expats would likely find local colleagues to be more understanding than expected. They say a decade of deflation and economic hardship has changed the Japanese mindset. "I think the Japanese had more of the group mentality decades ago, but not so much now," said Shin Tanaka, head of PR firm Fleishman Hillard's operations in Japan. "I think most [Japanese] people are staying because they think there is little risk."

A Japanese employee at a foreign investment bank said he wasn't bothered by the fact that some of his colleagues left last week. He felt the gap was narrowed by technology, anyway, allowing some who left to do their share. "It hasn't really been a problem," he said. "They're working remotely out of other countries in Asia."

Still, the return of the "flyjin" to Tokyo and other areas of Japan will likely be an issue for management to grapple with one way or another in the coming weeks.

"Most companies are trying to give some space to people on both sides to adjust: the people who feel they were abandoned and the foreigners who are coming back and feeling some initial tension," said Mr. Pink. "Within a week or so that may resolve itself."

—Alison Tudor and Kana Inagaki contributed to this article.

Write to Mariko Sanchanta at mariko.sanchanta@wsj.com