NEW YORK — Baseball's drug-testing program was threatened when federal prosecutors seized player records and samples four years ago, baseball commissioner Bud Selig said in a letter to Congress released today.

The seizure of the 2003 test results jeopardized the program's confidentiality and caused a delay in the start of testing in 2004, Selig and union head Donald Fehr told Reps. Henry Waxman and Tom Davis, leaders of the House Committee on Oversight and Government Reform.

"Major League players faced the realistic prospect of criminal prosecution based on evidence from a drug test that they were promised would be anonymous," 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's seizure still is under dispute. A three-judge panel of the 9th U.S. Circuit Court of Appeals in January largely upheld the government's actions, 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.

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

Because of the dispute, testing in 2004 didn't start until July 8. Testing for the more than 100 players whose records were seized didn't begin until Sept. 21, meaning those players could figure out they would be tested in the short window before then and the end of the regular season Oct. 3.

In his December report, baseball investigator George 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 Gene Orza, the union's No. 2 official, in September 2004.

Waxman and Davis asked Selig and Fehr last month 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," Fehr wrote. "Volunteering it would necessarily have required explanation of the litigation, which was under seal."

Selig also disclosed 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."