Baseball’s drug-testing program was threatened when federal prosecutors seized player records and samples four years ago, baseball commissioner Bud Selig and union head Donald Fehr said in letters to Congress released Thursday.

The seizure of the 2003 test results as part of the Bay Area Laboratory Co-Operative drug investigation contributed to a delay in the start of testing in 2004, Messrs. Selig and Fehr told the leaders of the House Committee on Oversight and Government Reform, Henry Waxman and Tom Davis.

The delay lasted until July. Major League Baseball’s executive vice president for labor relation, Rob Manfred, had told drug investigator George Mitchell that the stoppage was for a “short period,” a description that could become a matter of contention with the committee.

“Major League players faced the realistic prospect of criminal prosecution based on evidence from a drug test that they were promised would be anonymous,” Mr. Selig wrote in his June 27 letter, which was hand-delivered to the committee. “The seizure undermined representations made to players that drug testing records generally would be confidential. … It is no exaggeration to say that the seizure threatened the continued viability of the entire drug-testing program.”

The legality of the government seizures remain in dispute. A three-judge panel of the 9th U.S. Circuit Court of Appeals in San Francisco largely upheld the government’s actions in January, reaffirming a decision it made in December 2006. But the entire 9th Circuit has been asked to rehear the case, which could wind up at the Supreme Court.

“It is true that at this time that the MLBPA considered whether it was proper under the circumstances to go forward with the testing program,” Mr. Fehr wrote Wednesday. “After all, as a result of the searches and subpoenas, we could not assure the players that the fundamental promise of confidentiality made to them in the (drug agreement) would be, or even could be, honored. But the MLBPA decided not to pursue that position at that time, but instead to litigate the cases and then deal with the aftermath in bargaining.”

Baseball’s 2003 testing was a survey without penalties. Because more than 5 percent of the samples were positive, testing with discipline was triggered to start the following year.

Testing in 2004 didn’t start until July 8 — and not until Sept. 21 for the more than 100 players whose records were seized. The union insisted it have time to tell players individually they had been targeted.

Because testing had to be completed by the end of the regular season on Oct. 3, and players were tested only once that year, those players could figure out they would be tested in a short window.

“Delaying the testing had the positive effect of keeping players at risk longer,” Mr. Selig wrote. “The predictability created by the ever-shortening testing window was, therefore, inevitable.”

Messrs. Waxman and Davis asked Messrs. Selig and Fehr on June 12 to explain why the 2004 delay wasn’t disclosed when they testified during the March 2005 hearing on steroids, which became infamous when retired slugger Mark McGwire repeatedly evaded questions about performance-enhancing drugs.

“It was not responsive to any question that the committee asked, nor did it affect the truth or accuracy of any testimony,” Mr. Fehr wrote. “Volunteering it would necessarily have required explanation of the litigation, which was under seal.”

Mr. Selig’s response on that point was similar.

“No question was asked that would have prompted a disclosure of the delay of the tests,” he wrote. “All of the Major League Baseball witnesses answered the committee’s questions fully and accurately.”

Mr. Selig said that when Mr. Manfred spoke with Mr. Mitchell “he did not recall at the time that the broader delay of testing early in the season actually was caused by operational considerations unrelated to BALCO.” Mr. Selig listed the factors as the need to distinguish positives results from nutritional supplements that weren’t banned, establishing arrangements with a new lab in Montreal and obtaining new collection kits.

In his December report, Mr. Mitchell questioned whether players were tipped off about testing. He said a former player, whom he didn’t identify, claimed he had been given two weeks’ notice of a drug test by the union’s No. 2 official, Gene Orza, in September 2004.

Mr. Selig disclosed in his letter that not all of the 100-plus players whose records were targeted by government tested positive for banned drugs.

“There were more names on the list than the number of positive results reported under the program in 2003,” he wrote. “This is probably due to the fact that the government seized test results for samples that were positive for nutritional supplements such as androstenedione that were sold over the counter in 2003.”

Mr. Selig also said a list of players whose records were seized by BALCO prosecutors inadvertently was sent to Major League Baseball in 2004. Because MLB agreed with the union that it couldn’t see 2003 test results for individuals, management agreed with the union to destroy the list.

Mr. Fehr said the union believes 64 players on the government list were tested during the final weeks of the 2004 season, resulting in one positive.

Messrs. Waxman and Davis said in a joint statement they are reviewing the letters. They were both traveling Thursday and unavailable to be interviewed, their offices said.