SAN FRANCISCO – The government’s legal stance in an ongoing investigation of steroid use by Major League Baseball players could put at risk the privacy rights of all Americans who have ever taken a drug test, federal appeals court judges warned last week.

At a hearing on Tuesday here, members of a three-judge panel sparred with a Justice Department attorney over the government’s appeals of three lower court orders that found investigators went too far in searches carried out last year as part of a high-profile probe of a Burlingame, Calif., lab, the Bay Area Laboratory Co-Operative, or Balco. The lab provided performance enhancing compounds to a variety of athletes, including baseball sluggers Jason Giambi and Barry Bonds, and Olympic sprinter Marion Jones.

The disputed searches took place in April 2004 at two private facilities, Comprehensive Drug Testing of Long Beach, Calif., and a laboratory of Quest Diagnostics, in Las Vegas.

An attorney for the Major League Baseball Players Association, Elliott Peters, told the appeals court that federal agents brazenly exceeded the terms of the search warrants that were issued. “They had a very specific search warrant for 10.They seized the drug testing results for thousands of people,” he said.

The details of the warrants and nearly all other aspects of the dispute remain under seal. The appeals were first reported on Friday by Bloomberg News, but received no public attention earlier because they were not publicly docketed. They were identified in a public court calendar as “Seal 1 v. Seal 2.”The court did post a recording of the oral arguments last week on its Web site.

The Justice Department attorney, Erika Frick, said at the session that investigators on the steroid probe did only what they were permitted to do.

At least two of the appeals court judges sounded troubled by Ms. Frick’s argument that the government was entitled to pursue positive drug test results it came across during the searches, even if those involved were not among the 10 baseball players mentioned in the warrants. She said the situation was akin to finding a weapon or other evidence of crime in “plain view” while carrying out a search.

“The government’s position is, ‘Gosh, if we can get one test result, then we can look at everything else, and if it’s in plain view, we’re going to take that and investigate it wherever it leads,'” Judge Sidney Thomas said. “I don’t think anyone’s ever taken the position before. … It seems to me the natural implication of your argument is fairly staggering.”

In addition to Judge Thomas, the appeals are being considered by Judges Diarmuid O’Scannlain and Richard Tallman. “There’s got to be some sort of measurement or some rule that can be applied that will cabin this search,” said one judge on the panel, who could not be definitively identified from the audio recording. “You get to keep all 50,000 and you can do whatever you want? … That does not sound right to me.”

Ms. Frick replied that the government’s ability to use the data is restricted in a variety of ways. “There are all sorts of constraints,” she said.

While nearly all the records related to the searches remain secret, The New York Sun obtained a docket sheet from the federal court in Nevada that shows that in August 2004 Judge James Mahan granted a motion by the players’ association to return some items seized during an April 2004 search of Quest Diagnostics. The records show that the government asked Judge Mahan to stay his order. He refused.

The government appeared to be particularly upset with language used in a ruling by Judge Susan Illston of San Francisco, who heard a dispute about an aspect of the search. The specific criticisms of the government’s conduct are murky, but an appeals court judge and the players’ group lawyer, Mr. Peters, said some of the district court judges suggested that the government deliberately kept them uninformed about actions it was taking in other parts of the country.

“They felt the government had engaged in a game of hide the pea,” Mr. Peters said.

The searches required some coordination because the laboratory in Las Vegas had samples identified only by number, while the facility in Long Beach had data matching the numbers to specific players. According to press reports, the government attempted to seek the results and samples by subpoena in early 2004, but turned to search warrants after negotiations with the players’ association fell apart.

In July, the founder of Balco, Victor Conte Jr., and a personal trainer to Mr. Bonds, Greg Anderson, pled guilty to money laundering and distributing anabolic steroids. Conte received a four-month jail term, while Anderson was sentenced to three months. An Illinois chemist, Patrick Arnold, was charged in the case earlier this month and has pleaded not guilty. No athlete involved in the probe has been charged with a crime.