Three journalism organizations on Thursday protested a decision by the Obama administration to remove a database of physician discipline and malpractice actions from the Web.

The National Practitioner Data Bank, created in 1986, is used by state medical boards, insurers and hospitals. The “public use file” of the data bank, with physician names and addresses deleted, has provided valuable information for many years to researchers and reporters investigating oversight of doctors, trends in disciplinary actions and malpractice awards.

On Sept. 1, responding to a complaint from Dr. Robert T. Tenny, a neurosurgeon in Kansas, the Health Resources and Services Administration, an agency of the Department of Health and Human Services, removed the public use file from its Web site, said an agency spokesman, Martin A. Kramer. The agency also wrote a reporter a letter to warn he could be liable for $11,000 or more in civil fines for violating a confidentiality provision of the federal law. Both actions outraged journalism groups.

“Reporters across the country have used the public use file to write stories that have exposed serious lapses in the oversight of doctors that have put patients at risk,” Charles Ornstein, president of the Association of Health Care Journalists and a reporter for ProPublica, an investigative newsroom, said in an interview. “Their stories have led to new legislation, additional levels of transparency in various states, and kept medical boards focused on issues of patient safety.”

Two other national journalism organizations, Investigative Reporters and Editors and the Society of Professional Journalists, joined the health reporters’ group in a letter to Mary K. Wakefield, administrator of the federal office. “If anything, the agency erred on the side of physician privacy,” they wrote.

Mr. Kramer said the agency, contacted by a doctor, had become concerned that a Kansas City reporter obtained information from the full data bank, not just its public use file.

“We have in the past sent letters like this, but it is the first time in our knowledge one has gone to a journalist,” Mr. Kramer said.

That concern and the letter, though, were made moot when the reporter explained that he had been getting information from the public use file, Mr. Kramer said. “That’s the end of that,” he said.

Nonetheless the agency is reviewing the public use file and may change it to further assure confidentiality before placing it back on the Web, he said, adding that he hoped it would be public again within six months.

“We are going to do everything we can to get the data back up in a public use file as quickly as we possibly can,” Mr. Kramer said. “We want to make sure the public, researchers and reporters have access to all the information that we can legally make available.”

Mr. Kramer said he could not speculate about how the public use file would be changed. He said the agency was still reviewing complaints made by the journalist organizations.

The Kansas City Star, despite the letter to its reporter, published its article on Sept. 3, titled, “Doctors With Histories of Alleged Malpractice Often Go Undisciplined.”

“To see whether other doctors with long malpractice payment histories are practicing in Kansas and Missouri, The Star analyzed thousands of records in the National Practitioner Data Bank,” the article said. It found 21 doctors had at least 10 malpractice payments but had never been disciplined by the states.

Mr. Ornstein said the Star reporter, Alan Bavley, like many others across the country, had performed broad research of courts, state agencies and hospital actions, “allowing them to connect the dots” to individual doctors. But he said the federal database itself did not reveal identities.

Other recent notable articles based partly on the database have appeared in The Duluth News Tribune in Minnesota and The St. Louis Post-Dispatch, which published a series last year titled, “Who Protects the Patients?”

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