“It’s like comparing a microwave to a toaster,” said David Rudovsky, one of Dr. Xi’s lawyers. “They’re completely different technologies but, well, they both warm food. It was on that level that the government got the science wrong.”

A spokesman for the F.B.I. declined to comment on the lawsuit. Federal agents are immune from most lawsuits related to their jobs, and Mr. Haugen can argue that the lawsuit should be dismissed on that ground. Dr. Xi is suing for violations of his constitutional rights. The Supreme Court has said people can sue individual government employees like police officers and F.B.I. agents for such alleged violations.

Dr. Xi came to the United States in 1989 and is a naturalized American citizen. He has always maintained his innocence and said he knew the agents had conflated the evidence as soon as he heard it. “The very first word I said was ‘absurd,’” he recalled.

Dr. Xi said his arrest cast unwarranted suspicion over him and his work. He was suspended from his job, lost his title as the department’s interim chairman and was prohibited from entering campus or speaking with students. He said his arrest was part of a law enforcement mind-set that views Chinese-Americans as uniquely suspicious.

Prosecutors view Chinese espionage as a major threat, both to government secrets and valuable corporate information. Experts say the government in Beijing has an official policy encouraging the theft of trade secrets. Prosecutors have charged Chinese workers in the United States with stealing Boeing aircraft information, specialty seeds and even the pigment used to whiten Oreo cookie cream.

But the Justice Department has made several mistakes. In December 2014, prosecutors dropped charges against two former Eli Lilly scientists who had been accused of giving proprietary information to a Chinese drugmaker. Three months later, prosecutors dropped a case against a Chinese-American hydrologist who had been charged with secretly downloading information about dams.

Each case raised the specter of Chinese espionage without explicitly charging the suspects as spies. Because prosecutors cited routine crimes such as wire fraud, national security experts at Justice Department headquarters did not oversee the cases. Last year, the department issued new rules giving Washington greater control over such cases.