“N.I.H. has basically been operating on the principle that everyone is well intentioned,” said Scott Kennedy, an expert on China at the Center for Strategic and International Studies who briefed the N.I.H. working group. “Then they run smack dab into the challenge of China, which has millions of researchers scrambling for money and for fame and for national glory. That creates an environment where some people may feel pressure to skirt, ignore or break the rules.”

In some cases, Dr. Collins and Mr. Wray said, Chinese graduate students or visitors have taken intellectual property from American laboratories and given it to Chinese scientists or arms of the Chinese government, which published and commercialized the findings.

In other cases, scientists who received grants from the N.I.H. had shadow laboratories in China, which also received funds from the Chinese government. The foreign funding and affiliations were, in some cases, unknown to the National Institutes of Health and even to the American universities where the scientists worked.

Particularly worrisome to American officials was the finding that China had somehow obtained confidential information from applications for N.I.H. research grants. Under federal law, the N.I.H. uses an elaborate process of peer review to evaluate applications, and information in the applications — providing valuable insights into some of the world’s most advanced biomedical research — is supposed to remain confidential.

Congress has poured money into the institutes, which have a budget of $39 billion this year, up 30 percent from 2014, and lawmakers say the agency has been phenomenally productive. More than $4 out of every $5 is distributed to researchers around the country studying cancer, heart disease, diabetes and myriad other conditions.