Wall Street banks and tech companies big and small were scrambling on Saturday to figure out how their tens of thousands of employees would be affected by President Trump’s proclamation imposing a $100,000 fee for visas granted to skilled foreign workers.

The change set off immediate confusion over the exact rules and how they would be enforced. Shortly after Mr. Trump signed the proclamation on Friday, employees at Microsoft, Amazon and JPMorgan received notices advising those with H-1B visas who were outside the United States to return before the new rules take effect at 12:01 a.m. Eastern time on Sunday.

The Trump administration sought to address the confusion on Saturday by saying that the fee would only apply to new applicants, and renewals or current visa holders would not be affected. In a post on social media, the White House said the change would “not impact the ability of any current visa holder to travel to/from the U.S.”

Still, many executives, general counsels and human resources departments, as well as their immigration lawyers, said they were coming down on the side of caution this weekend. Several companies and attorneys had already urged workers to return to the United States as soon as possible. Many kept their eyes glued on the White House social media accounts for any pertinent clarification.

“We acknowledge that this is an uncertain time for our people on H-1B visas and your families,” Jacqueline Arthur, head of human capital management at Goldman Sachs, wrote in a memo on Saturday to employees. The memo said that Goldman was working with its lawyers “to review the specifics of the order as more detail becomes available to communicate with you accordingly.”

Bernhard Mueller, co-chair of the immigration practice group at Ogletree Deakins, said he had been flooded with calls from executives and corporate board members about the new rules and how to communicate with employees about them. “There’s a lot of question marks all over this,” he said early Saturday. “We are still flying in somewhat foggy conditions.”

Late Saturday, the U.S. Citizenship and Immigration Services issued a memo underscoring that Mr. Trump’s proclamation only applied “prospectively to petitions that have not yet been filed.”

Still, the policy change represents a significant overhaul of how the United States distributes what are known as H-1B visas. The visas, which play a crucial role in helping employers fill jobs in the tech industry and beyond, have been at the center of a deep immigration debate.

Immigration hard-liners contend that the visa program hurts Americans because companies have brought in foreign workers at lower wages, while many business leaders say the program helps American companies stay competitive.

White House officials said the policy change would help ensure that companies were giving priority to hiring domestic workers. “President Trump promised to put American workers first, and this common sense action does just that by discouraging companies from spamming the system and driving down wages,” Taylor Rogers, a White House spokeswoman, said in a statement.

But executives and industry trade groups said they worried about how the steep fee would affect businesses’ ability to fill critical positions. A spokesman for the U.S. Chamber of Commerce said the group was working with the Trump administration and its members to “understand the full implications and the best path forward.”

“We’re concerned about the impact on employees, their families and American employers,” Matt Letourneau, a spokesman for the chamber, said in a statement.

Amazon, Meta, Google, Apple and Walmart, which are among the biggest users of H-1B visas, either declined to comment or did not respond to a request for comment.

Adam Kovacevich, the founder and chief executive of Chamber of Progress, a left-leaning tech industry policy coalition, said he expected that firms would have to reassess their entire approach to the H-1B visa program, and he worried about how the change could affect the nation’s competitiveness in fields like artificial intelligence.

“I think this is going to mean that we’re fighting the A.I. war against China with one hand tied behind our back,” Mr. Kovacevich said. “There is a limited number of top talent in A.I., and some of that is foreign-born.”

The change was widely expected to be met with lawsuits. Jeff Joseph, the president of the American Immigration Lawyers Association, said the organization was working with other groups to file a legal challenge seeking a temporary restraining order as soon as this weekend. Mr. Joseph said the organizations had been making strategy calls over the weekend and working on finding plaintiffs who represent a wide range of industries.

Benjamin Johnson, the executive director of the association, said the group’s members were “dealing with chaos” as their clients have been scrambling to understand the change. “I’m just hearing confusion and panic,” he said.

Although tech companies receive the most H-1B visas, Mr. Johnson underscored that the new fee would also affect workers in the medical and manufacturing industries as well as at universities who receive H-1B visas. “The numbers of companies and industries where H-1B workers play a really critical role is incredibly broad,” he said.

Some workers who are currently abroad said they were unsure about how to immediately respond. A 29-year-old software engineer with a stamped H-1B visa set to begin in less than 20 days, was tucked into bed in his Munich apartment early Saturday when he realized he might be stuck in Germany.

Speaking before the government’s clarification on how the visa fee would be applied, the software engineer, who is an Indian citizen with a German work visa, said he felt “clueless” about how to proceed. He spoke on condition of anonymity because he was worried about his visa status.His company, he said, had told him to stay put.

In its email to employees on Friday evening, Microsoft, which has roughly 5,200 employees in the program, said that workers currently in the United States should remain there “for the foreseeable future,” even if it interrupts future travel plans.

“The critical thing is to stay in the U.S. in order to avoid being denied re-entry,” the advisory said.

Some policy experts praised the Trump administration’s change and said it would help ensure that companies are not suppressing wages or giving priority to hiring foreign workers over Americans. Lora Ries, the director of the Border Security and Immigration Center at the Heritage Foundation, a conservative think tank in Washington, said the $100,000 fee was a “good start” at reforming the H-1B program because it would make companies prioritize which foreign workers they want to hire.

“Americans aren’t getting a fair shake at the opportunities because too many employers are bending the system,” Ms. Ries said.

But the policy change also raised concerns about the long-term impact on the U.S. economy and corporate America. Venture capitalists warned that the change would add to concerns surrounding an uneven playing field, with only the nation’s largest companies being able to pay the fees or secure an exemption, as technology giants like Apple and Nvidia have already done with certain tariffs.

The challenges of complying may be particularly acute for start-ups, many of which operate for years without reaching profitability.

“There is not a single company that I have invested in the last 10 years that could afford to pay this,” said the venture capitalist and private equity investor Alan Patricof.

The government caps H-1B visas at 85,000 a year, and visa holders can also bring in their immediate family in a related program. The vast majority are typically granted to Indian citizens.

The Indian government issued a statement on Saturday saying that it was still determining “the full implications” of the new visa rules. But, the Ministry of External Affairs said, “This measure is likely to have humanitarian consequences by way of the disruption caused for families.”

Mukesh Aghi, chief executive officer of the US-India Strategic Partnership Forum, said he had been reaching out to some of the 450 companies in his membership for their opinion on the organization’s next steps.

“We understand our administration’s position that they want to avoid misuse of H-1B — and we support that,” Mr. Aghi said.

“But at the same time, we just want to make sure that in the process, companies which are creating jobs here do not get penalized.”

Karen Weise, Hamed Aleaziz, Eli Tan and Rob Copeland contributed reporting