A week before Christmas, Skylar Peak, a busboy at ZiZi, a Mediterranean restaurant in Chelsea, learned in a text message from his manager that a co-worker had tested positive for the coronavirus.

Mr. Peak took time off to be tested, and it took five days to get a negative report. During that time, several more employees at ZiZi tested positive. The owner closed the restaurant for a week because there weren’t enough people to run it.

ZiZi has reopened, like many New York City restaurants that temporarily shuttered in December during the sudden onslaught of the Omicron variant. But the decisive moves those businesses took last month, and in earlier stages of the pandemic, have given way to something murkier — a time in which both employees and owners are deeply unsure what to do when they or co-workers test positive for the virus. Keep working and risk infecting others? Call in sick and miss out on crucial income? Close the restaurant to protect staff and customers, or take steps to safeguard them and stay open?

Mr. Peak agreed with ZiZi’s decision to close last month, but the continuing uncertainties have left him feeling bewildered and frustrated. When Sharon Hoota, an owner of the restaurant, and a manager recently called the city’s 311 help line three times to ask what to do if a worker tested positive for Covid, Mr. Hoota said they received differing advice on how soon that person should be allowed to return to work.

While businesses throughout the country have had to...

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