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The F.B.I. agents spent nearly two years tailing the professor, following him to work, to the grocery store, and even keeping his college-age son under surveillance. They told the university where he held a tenured position that he was a Chinese operative, prompting the school to cooperate with their investigation and later fire him.

But the F.B.I. was unable to find evidence of espionage, according to an agent’s testimony in court.

Federal prosecutors pressed charges anyway, accusing Anming Hu of concealing his ties with a university in Beijing and defrauding the government in connection with research funds he had received from NASA. The trial ended in a hung jury. One juror called the case “ridiculous.” In September, a judge took the rare step of acquitting the Chinese-born scientist on all counts.

“It was the darkest time of my life,” Dr. Hu said in his first in-depth interview since being acquitted.

Universities in the United States once welcomed the best and brightest scientific talents from around the world. But government officials have become increasingly suspicious that scientists like Dr. Hu are exploiting the openness of American institutions to steal sensitive taxpayer-funded research at the behest of the Chinese government. It’s had a chilling effect across campuses that scientists and university administrators say has slowed research and contributed to a flow of talent out of the United States that may benefit Beijing.

In interviews with several scientists of Chinese descent working in American universities, a picture emerged of a community on edge. Some described being humiliated by mandatory training on foreign interference that featured only examples of ethnic Chinese scientists, and unexplained delays for visa renewals. They were all concerned that seemingly anything — a collaboration with another scientist from China, a slip-up on a disclosure form — could provide an opening for federal investigators to come knocking.

The trial of Dr. Hu, who worked at the University of Tennessee at Knoxville, is being held up as a clear example of government overreach. He was under house arrest for 18 months during the investigation with no job or income, reliant on GoFundMe donations for his legal defense fees. Neighbors and church friends delivered groceries and took out his garbage. While the university has since offered to reinstate his job, Dr. Hu, a naturalized Canadian citizen, said his immigration status remains in limbo.

“My basic human rights were invaded, my reputation was destroyed, my heart was deeply hurt, my family was hurt,” he said. “This is not fairness.”

A recent study conducted by the University of Arizona and the Committee of 100, an organization of prominent Chinese Americans, surveyed scientists of both Chinese and non-Chinese descent working at academic institutions in the United States on issues of race and ethnicity in science and research. Around half of the Chinese scientists surveyed — including some American citizens — said they felt they were being surveilled by the U.S. government. Some have blamed a law enforcement program called the China Initiative, which was started during the Trump administration and has continued under President Biden.

The program is aimed at preventing the Chinese government’s theft of American trade secrets and other acts of espionage. But scholars, scientists, civil rights groups and lawmakers have asked whether it has gone too far in targeting academics, especially since most research done at universities is unclassified and eventually published.

Nearly 2,000 academics at institutions including Stanford University, the University of California, Berkeley and Princeton University have signed open letters to Attorney General Merrick Garland expressing concerns that the initiative disproportionately targets researchers of Chinese descent and urging that the program be terminated.

“So much of our intellectual technological power is from immigrants,” said Steven Chu, one of the signers, a Nobel Prize-winning physicist at Stanford University and a former U.S. secretary of energy. “We’re shooting ourselves not in the foot but in something close to the head.”

Dr. Hu was the first academic charged under the China Initiative to stand trial. So far the F.B.I. has brought 12 prosecutions at universities or research institutions in three years, but none have involved charges of economic espionage or theft of trade secrets or intellectual property. Most involved allegations like wire fraud, lying to federal investigators and failure to disclose ties with China.

Behind the recent scrutiny of academics is a problem years in the making.

Over the past two decades, as federal funding for basic scientific research at universities stagnated, scientists sought alternative sources of money. Eager to expand their global footprint, American universities promoted collaborations with international peers, including in China. Beijing, which has set its sights on becoming a science and technology superpower, was happy to oblige.

Researchers took advantage of growing opportunities in China, including talent recruitment programs, lucrative consulting contracts, honorary titles and grants.

But the Chinese government sometimes used these relationships to steal or incentivize the transfer of intellectual property from American companies. As the Trump administration intensified scrutiny of espionage by China, it expanded the dragnet to include academic collaboration, prompting federal agencies that provide funding — and some universities — to step up enforcement of policies on the disclosure of foreign ties and conflicts of interest.

“There’s no room for xenophobia or ethnic profiling,” said Anna Puglisi, a senior fellow at Georgetown University’s Center for Security and Emerging Technology. “But what gets lost in the discussion is the bigger question that we need to be asking, which is: ‘Do we have the system in place to mitigate the behavior and central government policies of a nation state that are specifically set up to target the seams in our system?’”

To some, the intensified scrutiny amounted to overreach.

Many scientists have expressed frustration over what they say are shifting and overlapping disclosure guidelines from universities and funding agencies that make it hard to avoid getting caught in the F.B.I.’s web. During Dr. Hu’s trial, for example, it emerged that both NASA and the University of Tennessee at Knoxville had provided unclear rules on how he should disclose foreign ties.

“I don’t think anybody doubts the Chinese government and C.C.P. are engaged in economic espionage and other malign behaviors,” said Michael German, a fellow at New York University’s Brennan Center for Justice and a former F.B.I. agent. “So that’s where the U.S. government should focus its resources, instead of trying to grab easy statistical accomplishments by targeting college professors who have nothing to do with Chinese espionage.”

A Justice Department spokesman said the department was dedicated to countering Chinese efforts to undermine national security, but that the department also took concerns about discrimination seriously.

For now, unease is growing. Yiguang Ju, a professor of mechanical and aerospace engineering at Princeton and a naturalized U.S. citizen, said it had been the honor of a lifetime in 2010 when NASA asked him to help develop a plan for the future of American rocketry.

If he were to receive the same invitation today, he would decline, he said. The spotlight on Chinese scientists at academic institutions was too great, and the pride of working with the agency not worth the possible risk to him and his family. “It’s not because I don’t want to serve,” he said. “I’m scared to serve.”

That fear comes as China has started to experience a reverse brain drain. Over the last decade, a growing number of Chinese scientists have been lured back to the country by the promise of ample funding, impressive titles and national pride. More recently, scientists returning to China have cited a hostile environment in the United States as a factor.

Westlake University, a research university in the eastern Chinese city of Hangzhou, has recruited an impressive roster of talent, including many who once held faculty positions at top American schools. In August, Westlake announced several new hires, including a tenured professor from Northwestern University and another from the University of Illinois at Urbana-Champaign.

Shi Yigong, a prominent molecular biologist and the president of Westlake University, said colleagues had complained about the atmosphere of suspicion in the United States. “For those who have chosen to relinquish their jobs in the U.S., sometimes I do hear stories of a bitter nature,” Dr. Shi said. “I think some of them, not all of them, have been singled out for what I think was pretty harsh treatment.”

At least one person, though, is determined to stay in the United States: Dr. Hu.

The son of a factory worker, he grew up in a poor village in the eastern Chinese province of Shandong and said his interest in science began at a young age. In elementary school, he rigged a simple radio by wiring a speaker with scrap mineral and connecting it to a makeshift antenna he hung from a tree.

After earning advanced degrees in China, he left the country in 1997 with his wife and worked in several countries before obtaining a second Ph.D. in physics in Canada. Like countless immigrants before him, he moved to the United States in 2013 with hopes for a better life and career.

He has sacrificed too much to give it all up now, he said.

He would rather stay in the United States to contribute not just to science, his first love, but also to his new passion: promoting justice. “I have no interest in politics and know almost nothing about it,” he said. “But I know that targeting Chinese and Asian Americans — that will not make the United States strong.”

Javier C. Hernández and Amy Chang Chien contributed reporting.