Updated at 3:57 p.m.

A judge set bail for the head of Harvard's chemistry department, who was arrested earlier this week for allegedly lying about his ties to China, at $1 million on Thursday after the professor appeared in federal court.

Acclaimed scientist Charles Lieber, who prosecutors allege lied about his acceptance of more than $1 million in research funding from the Chinese government, has five days to post the bail and has been ordered by Magistrate Judge Marianne Bowler not to travel outside of Massachusetts.

Lieber appeared in court Thursday, in handcuffs and wearing an orange jumpsuit. Bowler had twice denied bail for Lieber — once on Tuesday and once Thursday morning during an earlier proceeding before his wife appeared in court.

Court documents show Lieber was earning as much as $50,000 a month from a Chinese university and hiding his income from Harvard, the Department of Defense and the National Institutes of Health.

Harvard put Lieber on paid administrative leave Tuesday and Bowler denied him bail, ordering him to stay in U.S. custody after prosecutors argued he's a “serious flight risk.”

Prosecutors also want Lieber to surrender access to foreign bank accounts and his passport, and are asking that he and his wife not make significant cash withdrawals or contact Chinese government and university officials.

While Lieber’s arrest is not unprecedented, college leaders say charges against a researcher of his caliber is highly unusual. He is chairman of Harvard's chemistry department and a tenured university professor, the highest rank for one of its faculty members.

Lieber's arrest shocked both the scientific and Harvard communities. There has been growing suspicion of Chinese students on college campuses in the U.S., and some faculty worry this case is going to make it worse.

Many in the scientific community suspect investigators are racially profiling students and faculty. Lieber, who is white, is the first non-Chinese scientist to be charged in what some are calling a new "Red Scare" on campus. And many schools in the Boston area say their international students were already experiencing new delays in processing visas to continue their career training.

Harvard requires all faculty members to submit annual reports to the Faculty of Arts and Sciences, including disclosure of any potential conflicts of interest.

The NIH has similar requirements and any payments from a foreign or domestic university or government must be declared to the Internal Revenue Service.

In a statement to WGBH News, the NIH said in recent years, the agency has been made aware of subversive efforts by foreign entities to target U.S. scientists and undermine the integrity of their research.

“These activities are the antithesis of collaboration,” the statement said.

In August of last year, Harvard’s vice provost for research, Richard McCullough, sent a letter to all faculty, alerting them to be “cognizant of increased scrutiny of information submitted to federal agencies.”

A National Science Foundation report released in December on the fundamentals of research security said that actions of the Chinese government have raised concerns about foreign influence in the U.S. academic sector.

After reviewing classified and open-source evidence, the NSF report concluded “the scale and scope of the problem remain poorly defined, and academic administrators, faculty, and front-line government agencies lack a common understanding of foreign influence in U.S. fundamental research and potential risks.”

The report recommended that failures to disclose potential conflicts of interest should be investigated by federal agencies and universities as likely violations of research integrity.