The National Institutes of Health and some leading universities, such as Harvard and Stanford, have suffered black eyes this year because of revelations that researchers with federal grants failed to disclose secret payments that they took from pharmaceutical companies.

The NIH was warned about the dangers of the problem years ago by one of its own scientists, Ned Feder, who wrote letters to several publications suggesting that the agency require its grantees to publicly disclose money they earn from medical companies. Instead of heeding Dr. Feder’s advice, the agency punished him.

In 2005, Mr. Feder wrote a short letter to Nature arguing that the current system kept important information away from the public. “NIH-funded researchers are required to provide details of any consulting arrangements to their universities, which in turn approve or veto the plans,” he wrote. “This information is confidential and usually cannot be seen by the public.”

Dr. Feder went on to suggest that “the NIH could require grantees to make public disclosures of their paid arrangements with pharmaceutical, investment, and other companies, as well as their ownership of stock and stock options, as a condition of having their medical research funded by the government.”

The agency formally reprimanded Dr. Feder for writing to Nature and identifying himself in the letter as an employee of the NIH. Dr. Feder protested the reprimand, and it was subsequently removed, without explanation.

While Dr. Feder was unable to change the system, Sen. Charles E. Grassley of Iowa is having more success. The Republican senator’s investigators obtained records from pharmaceutical companies of payments to academic researchers. Several prominent psychiatrists failed to disclose many of those payments to their universities.

In August the NIH froze financial support of a $9.3-million grant to Emory University because of payments made to the leader of the grant project, Charles B. Nemeroff. The agency is demanding to see all the financial disclosures of grantees at Emory and how the university is dealing with conflicts of interest.

“The NIH has shown no interest in reforming its policies unless they’re forced to do it,” said Dr. Feder, who is now staff scientist at the Project on Government Oversight.

The NIH declined to comment on Dr. Feder’s case, saying it does not discuss personnel matters. —Richard Monastersky