SAN FRANCISCO — A divided appeals court panel has upheld the right of federal investigators to examine positive drug testing results for more than 100 professional baseball players as part of a probe of illegal steroid use by athletes.

The 9th Circuit Court of Appeals decision issued yesterday rejected the rulings of three district court judges who found that the government acted improperly when seeking and carrying out grand jury subpoenas and search warrants in 2004 against California and Nevada laboratories that handled players’ drug tests.

“We are aware of no authority that the simultaneous pursuit of search warrants and subpoenas in aid of an ongoing grand jury investigation constitutes a violation of the Fourth Amendment,” Judge Diarmuid O’Scannlain wrote in the appeals court opinion, which was joined by Judge Richard Tallman. “We see no evidence of bad faith or pretext here.”

After the Major League Baseball Players’ Association and one of the labs objected, the government limited its subpoenas to records pertaining to 11 players the government suspected of drug use. However, after seizing some of the labs’ computer records, the government claimed the authority to pursue positive results it discovered for more than 100 athletes.

If the new ruling stands, federal authorities could broaden their probe beyond the list of players targeted in the searches and subpoenas. That roster reportedly included Jason Giambi of the New York Yankees and Barry Bonds of the San Francisco Giants, both of whom have denied knowingly using steroids.

Judge O’Scannlain concluded that prosecutors had the right to hang onto and use all information in spreadsheets of a few pages, though he said safeguards would be needed for larger databases. He found that the lower court judges were wrong to grant motions to return the data on the athletes not named by the government.”Return of property should follow only a particularly egregious violation,” Judge O’Scannlain wrote.

The third judge on the appeals court panel, Sidney Thomas, filed a scathing dissent warning that computer-based files were being opened to wholesale rummaging by the government.

“The scope of the majority’s new holding in the digital age could not be greater; it removes confidential electronic records from the protections of the Fourth Amendment,” Judge Thomas wrote. “The stakes in this case are high. The government claims the right to search — without warrant or even a suspicion of criminal activity — any patient’s confidential medical record contained in a computer directory so long as it has a legitimate warrant or subpoena for any other individual patient’s record that may be contained as part of data stored on the same computer.”

The majority suggested that a magistrate could divide up the records if someone objected to a search or a subpoena, but Judge Thomas pointed out that third parties, such as the 13 other sports leagues and three competitions swept up in the government’s baseball-related quest, might never know their privacy was at stake. “At least until this opinion has been issued, no one in the National Hockey League knew that the government had seized medical records pertaining to its players without a warrant,” Judge Thomas wrote.

Judge Thomas said that, in order to get the search warrants, the government falsely suggested that the computer files may have been booby trapped. Prosecutors also failed to disclose that one of the labs, Comprehensive Drug Testing of Long Beach, Calif., had agreed to preserve all its data, the Judge wrote.

However, the majority rejected the claim that law enforcement agents misled the lower courts about the potential consequences of delaying the searches. “The government never claimed in its affidavits that any evidence was in danger of being destroyed,” Judge O’Scannlain wrote.

Attorneys involved did not return phone calls yesterday. A receptionist at one of the labs referred a reporter to a Major League Baseball labor relations executive, Robert Manfred Jr., who did not respond to an e-mail message. The players or the labs could seek relief from the Supreme Court or ask that a 15-judge panel of the appeals court hear the case.

The district court proceedings took place in near-complete secrecy, at the request of all of the parties who appeared. The appeal became public only because the judges rejected a request by both sides to seal the courtroom during arguments last year.

In their 115-page ruling yesterday, the appeals judges ordered the lower courts to take up this reporter’s motion, filed more than a year ago, to open the court filings and decisions to the public. Calling the secrecy “regrettable,” Judge Thomas said not all of the information in the case was required to be kept private under grand jury rules. He said the parties managed to “circumvent” procedures designed to keep the courts open to the press and the public.

Judge O’Scannlain was appointed by President Reagan. Judges Tallman and Thomas were appointed by President Clinton.

An appeal by two San Francisco Chronicle reporters who have refused to testify in the steroid probe is pending before the 9th Circuit. A district court judge has ordered that the pair, Mark Fainaru-Wada and Lance Williams, be jailed for contempt, but they are free while the appeal goes forward.