The chemistry professor’s nightmare seemed to finally be over.

Five years had passed since Feng Tao, also known as Franklin, was led by F.B.I. agents out of his home in Lawrence, Kansas. The first professor to be arrested under a Trump-era program aimed at fighting Chinese economic espionage, Dr. Tao was accused of hiding his ties to a Chinese university while conducting federally funded research at the University of Kansas, where he was tenured.

In July, he won his legal fight. A federal appeals court overturned the final conviction in his case. His wife, Hong Peng, recalled in an interview that she thought her husband could finally return to his lab, and their family could perhaps recover some semblance of a normal life.

But the University of Kansas has not reinstated him.

Dr. Tao, a Chinese citizen and permanent U.S. resident, is now suing his former employer for wrongful termination. He has accused the university of unlawfully surveilling him on behalf of federal investigators and of violating its own faculty disciplinary policies by terminating him before his criminal proceeding concluded.

“The university allowed itself to join in fearmongering and racist witch hunting,” read a complaint filed by Dr. Tao’s lawyers in January in a federal court in Kansas.

The University of Kansas did not respond to requests for comment.

Critics of the Trump program say that Mr. Tao is an example of how issues in the integrity of academic research have been leveraged to support accusations of espionage.Credit…University of Kansas

Dr. Tao’s experience underscores how, more than three years after the Justice Department officially ended the Trump-era program, known as the China Initiative, its impact is still reverberating among professors and researchers of Chinese descent.

The F.B.I. brought at least a dozen prosecutions at universities or research institutions over the three years the initiative was in effect, mostly against scholars of Chinese descent. None involved charges of economic espionage or theft of trade secrets or intellectual property.

Critics argued that the program had singled out scientists based on their ethnicity and overreached by blurring the line between violations of disclosure policies and more serious crimes like espionage. Many of the prosecutions against academics of Chinese descent eventually collapsed.

Yet there are growing concerns that the China Initiative could be revived under a second Trump administration.

Congress is currently considering an appropriations bill that would allocate funding for a Justice Department program focused on rooting out Chinese espionage, including in academia. And about a week ago, Republican lawmakers reintroduced legislation to protect against Chinese espionage by establishing a “CCP Initiative” — referring to the Chinese Communist Party — under the Justice Department.

“President Joe Biden recklessly ended the China Initiative that President Trump established during his first term,” Senator Rick Scott of Florida, the bill’s co-sponsor, said in a statement. “Now, President Trump is back in action to hold Communist China fully accountable for its exploitation of the United States.”

There is broad agreement that the Chinese government has tried to steal American technology, including through the recruitment of overseas scientists.

Chinese partnerships with U.S.-funded researchers and universities have also helped propel Beijing’s advancements in fields like hypersonics and nuclear weapons, artificial intelligence and semiconductors, according to a report put out last fall by a House committee focused on threats from China.

American universities disputed parts of that report, but they have also begun shuttering collaborations with Chinese institutions. In January, the University of Michigan ended its joint partnership with a Chinese university.

Lawmakers have also raised concerns about the large number of Chinese students studying science and engineering on American campuses — sometimes using rhetoric that has been criticized as fearmongering.

“The difference is, Chinese students here in the U.S. are not studying ancient Greek history — they’re here studying STEM and national security issues,” Senator James Risch, the Republican chairman of the Senate Foreign Relations Committee, said in January. “And each one of them, whether they like it or not, is an agent of the Chinese Communist Party.”

Critics say resources could be better directed at rooting out actual Chinese espionage threats. Such programs could also backfire on U.S. national security by helping accelerate an outflow of talent that is key to maintaining a scientific and technological edge against China.

“There are real, genuine threats that need to be addressed, but we should not be using a sledgehammer on the issue — we should be using a scalpel,” said Gisela Perez Kusakawa, executive director of the Asian American Scholar Forum, an advocacy group based in New York.

A 2022 survey of scholars of Chinese descent found that 45 percent of respondents who had previously obtained federal grants said they would avoid doing so in the future. In interviews, many cited concerns that it could subject themselves to unnecessary racial profiling.

The number of academic collaborations between researchers in the United States and China has also declined since 2017. And there are concerns that blanket restrictions on future research collaborations, such as the ones House Republicans recommended in their fall report, could cut American scientists off from areas where China is already ahead, such as materials science, hypersonics and nanotechnology.

Caroline Wagner, a professor of public policy at the Ohio State University who advises the government on research security, said that given the open nature of scientific research, efforts to blunt China from getting certain technologies could ultimately prove “shortsighted.”

Federal funding agencies and universities have recently taken steps to clarify which ties academics need to disclose, which Dr. Wagner said was a step in the right direction.

“I’m not sure there would be a need for the China Initiative now given all of the infrastructure that’s being put in place,” she said.

Critics say that Dr. Tao is a case study of how issues of integrity in academic research have been leveraged to support accusations of espionage. Raised in a village in southwest China, Dr. Tao moved to the United States in 2002 to pursue a Ph.D. in chemistry at Princeton University. After working at several different universities, he was recruited by the University of Kansas in 2014 to a tenured faculty position.

Known among colleagues for his intense work ethic, Dr. Tao continued to work after the allegations came out even while suspended without pay, publishing dozens of papers. But he has also accumulated millions of dollars in legal bills.

According to his lawsuit against the university, the F.B.I. began its investigation after a disgruntled visiting scholar falsely accused Dr. Tao of being a spy. During the investigation, authorities discovered a job offer from Fuzhou University in southern China that Dr. Tao had failed to disclose to the university.

Dr. Tao did travel to China to set up a laboratory and recruit staff for the university, while telling University of Kansas officials that he was in Germany. But Dr. Tao told the officials that he did not have anything to disclose, since he never received money or signed an employment contract with Fuzhou University.

Still, prosecutors said that Dr. Tao had committed fraud by hiding the offer and his work with the Chinese institution from his university and two funding agencies, the National Science Foundation and the Department of Energy.

A jury found him guilty on three counts of wire fraud and one count of making a false statement. But in 2022, a federal judge threw out the fraud convictions, citing insufficient evidence that Dr. Tao had received any money for his work in China.

“This is not an espionage case,” said U.S. District Judge Julie Robinson. “If it was, they presented absolutely no evidence that was going on.”

And in 2024, a federal appeals court voided the last count of making a false statement, arguing that Dr. Tao’s failure to disclose had not influenced an actual funding decision.

In his lawsuit to get his job back, Dr. Tao accused the university of discrimination based on race, saying that other professors who were not of Chinese descent did not face termination even though they had similar undisclosed interactions with foreign universities. The university, the lawsuit said, violated its own policies by failing to hold a hearing on his employment status.

In addition to reinstatement, Dr. Tao is seeking payment for lost wages, lawyers’ fees and damages for emotional distress and injury to his reputation.

“We can’t choose the country where we were born, where we came from,” said Dr. Tao’s wife, an American citizen. “What we have experienced, this is completely racial profiling.”