Rob Larew, the president of the National Farmers Union, said even talk of restrictions on immigrant farm workers was disruptive. “It just adds to an already stressed food system,” he said.

“If we do not have enough workers at the front end of that, it just adds more challenges to folks that need to get the food,” he added.

As late as Monday night, after Mr. Trump’s tweet, top White House officials said they believed the president’s order would apply to some of the guest worker programs, while exempting others. By Tuesday afternoon — amid the business backlash — officials acknowledged that devising an order that applied to some guest workers but not others would be overly complicated, and they abandoned it.

Mr. Trump said that his “pause” in immigration “will not apply to those entering on a temporary basis,” a reference to the worker visas, though he hinted that could change. “We want to protect our U.S. workers,” he said, “and I think as we move forward, we will become more and more protective of them.”

The decision to maintain most temporary work visas is certain to please business executives, but it will disappoint anti-immigrant groups, which have long called on the president to put an end to the guest worker programs they view as robbing Americans of jobs. And it could undermine Mr. Trump’s message to voters, many of whom are angry about competition from the foreign workers brought into the United States through those programs.

In recent weeks, the Trump administration has used health concerns to justify aggressively restricting immigration. Even before Tuesday’s announcement, the administration had expanded travel restrictions, slowed visa processing and moved to swiftly return to their home countries asylum seekers and undocumented immigrants who cross the border, alarming immigration advocates who have said that Mr. Trump and his advisers are using the pandemic to further hard-line immigration policies.

The president’s new executive order, which he could sign as early as Wednesday, will further close off the United States to tens of thousands of people seeking to live and work in the country, a move intended in part to stoke populist anger among his core supporters as he heads toward Election Day in November. Last year, about one million people were granted legal permanent resident status, commonly referred to as a green card.