The US Department of Education has opened investigations into whether Harvard and Yale universities failed to properly report hundreds of millions of dollars in foreign gifts and contracts, signaling a widening probe by federal agencies into whether China, Russia, and other countries have gained inappropriate influence and access into American academia.

Harvard and Yale received lengthy letters from the department on Monday requesting information about their foreign ties and funding, along with the safeguards they deploy to meet regulations. The letters come just weeks after a prominent Harvard scientist was arrested on charges that he lied to federal authorities about his alleged ties to China.

“If colleges and universities are accepting foreign money and gifts, their students, donors, and taxpayers deserve to know how much and from whom,’’ said US Education Secretary Betsy DeVos in a statement. “Moreover, it’s what the law requires. Unfortunately, the more we dig, the more we find that too many are underreporting or not reporting at all.’’

The arrest last month of Charles Lieber, Harvard’s chemistry department chair and a world-renowned nanoscientist, in particular has raised red flags about whether the university has proper oversight of these foreign engagements, education officials said.

Lieber, 60, was charged with making a false statement to federal authorities about his participation in the communist country’s Thousand Talents Plan. The plan seeks to attract foreign-educated scientists to China. According to court documents, Lieber was to be paid $50,000 a month, $158,000 in living expenses, and $1.5 million to establish a research lab at a Chinese university.

Lieber, who has been placed on administrative leave by Harvard, kept those ties secret from the university, according to federal prosecutors.

The education department has asked Harvard for all its records relating to the Thousand Talents Plan dating back to January 2012. But the investigation appears to go far beyond that — with the federal agency also seeking information about the university’s relationship with the governments of Qatar, Saudi Arabia, and Russia, and any solicitation of gifts from foreign sources.

The letter to Harvard did not specify how much money the government believes the university failed to report. It did, however, cite Harvard’s ties to disgraced financier Jeffrey Epstein as another example of poor oversight.

The education department has requested similar information from Yale and has said the school may have failed to report at least $375 million in foreign gifts and contracts, choosing not to report any gifts and contracts over the last four years.

Officials from Harvard and Yale said their universities are reviewing the letters and will be preparing to respond to them.

The Wall Street Journal first disclosed the Harvard and Yale investigations. The Journal reported that the education department is worried that the universities are “multi-billion dollar, multi-national enterprises using opaque foundations, foreign campuses, and other sophisticated legal structures to generate revenue.’’

Federal agencies and lawmakers from both parties have been warning for years that American universities, their scientists, and the ground-breaking research they do are particularly vulnerable to foreign influence. Foreign governments are using these campuses and their faculty to siphon intellectual property and academic research to gain a competitive edge against the United States, the federal government has cautioned.

US agencies have been particularly concerned about China. The FBI has about 1,000 investigations involving China’s attempted theft of US-based technology, Christopher Wray, the agency’s director, said at a conference last week.

National funding agencies, including the National Institutes of Health and the Department of Defense, are also investigating whether US academic researchers they give grants to are receiving money from foreign sources. The agencies have warned universities that their access to much-needed federal grants could be at risk if their scientists run afoul of foreign funding reporting requirements.

Colleges and universities have been left scrambling to address what has become a growing government concern. Scientists and researchers have also grown concerned that collaborations that have long-been commonplace are now under suspicion. Some scientists and academics have worried that this crackdown on foreign ties will chill research.

The education department has said that these investigations are about transparency and have already unearthed problems. Since July 2019, colleges and universities have reported about $6.5 billion in previously undisclosed foreign money, the agency said.

Foreign countries may be “seeking to project ‘soft power,’ steal sensitive and proprietary research and development data and other intellectual property, and spread propaganda benefiting foreign governments,’’ the education department said.

The education department in the past year opened probes into 10 universities, including the Massachusetts Institute of Technology, Boston University, and Cornell University, citing similar problems with reporting foreign engagements. A preliminary investigation found that those institutions reported $3.6 billion of previously undisclosed foreign gifts, the education department said.

On Tuesday, Republican Senator Rob Portman of Ohio and Tom Carper, a Democrat from Delaware, released a joint statement calling on American universities to be more transparent about their ties with foreign governments.

They called the billions of dollars already uncovered in unreported foreign gifts “shocking and unacceptable.’’

Deirdre Fernandes can be reached at deirdre.fernandes@globe.com. Follow her on Twitter @fernandesglobe.