(Bloomberg) -- Donald Trump came into office promising a restrictive new approach to immigration and there has been little question about his intention to follow through — with one seeming exception. Despite its enthusiastic rhetoric about the H-1B program, which provides temporary visas to high-skilled workers, the administration failed to make significant changes in time to impact the program’s annual lottery this April, leaving some who had anticipated action fuming. It has also declined to take up any of the legislative proposals for H-1B overhaul.

But a crackdown has been in the works, albeit more quietly. Starting this summer, employers began noticing that U.S. Citizenship and Immigration Services was challenging an unusually large number of H-1B applications. Cases that would have sailed through the approval process in earlier years ground to a halt under requests for new paperwork. The number of challenges — officially known as “requests for evidence” or RFEs — are up 44 percent compared to last year, according to statistics from USCIS. The percentage of H-1B applications that have resulted in RFEs this year are at the highest level they’ve been since 2009, and by absolute number are considerably higher than any year for which the agency provided statistics.

The H-1B program is controversial largely because IT firms based in India have used it to hire for rote computer programming jobs. These firms, like Infosys Ltd. and Tata Consultancy Services Ltd., have been working to reduce their reliance on the program, in anticipation of a less receptive political landscape. The overall number of H-1B applications dropped this year for the first time in five years. The skeptical eye the government is taking to applications has extended to all types of employers, according to immigration lawyers. Many are rethinking their own use of H-1B as a result.

It’s unclear how many applications are actually being rejected. In the meantime, the uncertainly alone is taking a toll on those who rely on the visas to work. Some applicants whose cases remained unresolved by Oct. 1, the annual effective date for new visas, have been sent home from their jobs. There are no official statistics tracking how many people are in this situation, but multiple immigration lawyers said this is the first year they’re seeing it occur in any significant numbers.

Even though Silicon Valley sees the H-1B program as one of its top political priorities, this campaign of reform by red tape has avoided the frantic political fights surrounding other aspects of immigration, like the proposed travel ban or the cancellation of DACA, a program for those who came to the country as undocumented children. After the recent terrorist attack in New York, Trump called for the elimination of another visa lottery program – the Diversity Visa Lottery – saying immigration should be merit-based. This mirrors past calls his administration has made to eliminate the H-1B lottery as a way to punish those who use it improperly.

Instead, says Peter Roberts, an immigration lawyer whose clients include large multinationals and startups, the administration is punishing everyone. He said many of this year’s challenges were “beyond ridiculous, trumped-up requests — no pun intended — issued either without legal basis or making no sense from a common sense standpoint,” and questioned whether they’d stand up. “How do you change the way we live? You can change the laws, or you can change the way we interpret them,” he said. “This is the latter.”

For Centro, a company in Chicago that makes technology for ad agencies, the problems started this summer. Centro had applied for visas for three young employees who already had the legal right to work for a limited time after graduating from college. One of the applications had been chosen in the H-1B lottery. Emilie Clark, the company’s director of human resources, happily called the employee to tell him his immigration status was settled for the next three years.

But the employee called Clark back in August, terrified that something had gone wrong. He’d received a letter from USCIS saying it would reject his application unless Centro proved the position required someone with specialized skills. Clark was surprised. She’d been helping people apply for visas for four years, and this was the first time she’d ever seen such a letter.

To Clark's eyes, the position — which consisted of writing algorithms and required knowledge of multiple programming languages as well as a solid understanding of relational data storage systems — wasn’t a borderline case. He had ended up at Centro after it hired a former manager of his, who recruited him to join the company. Clark pulled together everything the agency asked for as quickly as she could, but the employee’s status is still in limbo. (He continues to work on his initial visa.)

The man, who was born in India and went to school in the U.S., declined an interview request and asked not to be identified by name. “Every employee that we have on an H-1B, or going for any visa, they’re all really nervous,” Clark explained. Other employers and workers facing RFEs also declined to speak on the record because they were concerned doing so would impact their unresolved cases.

“We’re entering a new era,” said Emily Neumann, an immigration lawyer in Houston who has been practicing for 12 years. “There’s a lot more questioning, it’s very burdensome.” She said in past years she's counted on 90 percent of her petitions being approved by Oct. 1 in years past. This year, only 20 percent of the applications have been processed. Neumann predicts she’ll still have many unresolved cases by the time next year’s lottery happens in April 2018.

USCIS declined an interview request, sending a written statement instead. “USCIS officers use currently existing policy that interprets existing statutory and regulatory requirements to evaluate petitions and make an eligibility determination,” it said. “As done in the past, officers evaluate each petition on a case-by-case basis to determine if a petition qualifies for the benefit being requested.” Critics of the program have always called for stricter scrutiny of applications, which fit into Trump’s broader promise for “extreme vetting” of all potential immigrants.

There are ample signs that the Trump administration has a broader overhaul in mind. It staffed the USCIS with those who worked for Republican Senator Chuck Grassley of Iowa, a longtime critic of H-1B visas who in January proposed scrapping the H-1B lottery altogether in favor of a system prioritizing higher-paid jobs. A spokesperson for USCIS says that plan is still being considered. In April, Trump issued an executive order asking federal agencies to increase their scrutiny of the program. In a briefing with reporters at the time, a senior administration official floated the idea that administrative steps like raising application fees could also serve to reshape the program without the need for new laws or regulations.

Dick Burke, the CEO of Envoy, a Chicago-based immigration services firm, said many of his clients feel besieged by RFEs, which have more than doubled, and site visits, which are also up significantly. “I never try to divine the intent of anyone, particularly in terms of this administration,” he said. “But the sentiment of our customers is that they’re looking for ticky-tack violations to make things more difficult.”

Many employers have spent the last year musing whether they can continue to rely on the H-1B program at all. Clark of Centro says the company is considering relocating some employees who are having visa problems to offices overseas.

Venkat Narayanan, a partner at Aegis Company, a small software and consulting firm in the Seattle area, says his experience this year has left him afraid of the H-1B program. It’s always been a long shot. Aegis applied for a half-dozen visas this spring, and only one of them made it through the lottery. The year before, Aegis secured a visa for someone filing a type of job he’s filled with H-1B workers in the past. So Narayanan set up a client project for the prospective new employee, a woman who was living in Dehli, India, at the time.

USCIS challenged the application in August, which irked Narayanan because he had provided everything the agency had asked for. Narayanan was doubly annoyed because, without someone else to handle the new contract, it fell to him directly. For the last month, Narayanan has been spending four or five hours each morning doing the work himself, forgoing his own primary responsibility, which is to bring in new clients. “We might not make the profit we were expecting because of these issues,” he said. “We are afraid of on-boarding new H-1B employees, because of the unknown world.”

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