The Justice Department, following what many viewed as a balk Wednesday by the prosecution's top witness, may be scrambling to avoid another loss in its efforts to score a perjury conviction against baseball great Roger Clemens.

Clemens is facing charges that he lied under oath when testifying before Congress in 2008 that he didn't use performance-enhancing drugs.

The government fouled out in its original attempt to try Clemens in 2011 after a Justice Department attorney introduced an inadmissible piece of evidence. Federal Judge Reggie Walton quickly declared a mistrial amidst allegations of prosecutorial misconduct.

Many thought that would absolve Clemens, but the government decided to make it a double-header.

This week a beefed-up team of prosecutors is taking another swing at Clemens, but his former teammate Andy Pettitte may have complicated that effort during his testimony on Wednesday.

Up to this point, Pettitte had maintained that Clemens confided in him regarding the use of human growth hormone, or HGH. But under cross-examination this week, Pettitte threw the prosecution a curve ball when he admitted that there was a 50-50 chance he misunderstood the conversation with Clemens.

And during cross-examination Thursday, agent Jeff Novitsky -- who obtained syringes and cotton balls allegedly with Clemens' DNA on them -- admitted he has no personal knowledge what happened to those items before they came into his possession. The defense has called this evidence fabricated "garbage."

After a series of questions and objections from the prosecution, Judge Walton, who also is presiding over the retrial, asked Novitsky, "[Do you] know what the circumstances were regarding that evidence before you got it .. based about your own faculties?"

"No," Novitsky said.

Court watchers say another loss will only intensify criticism of the Justice Department for going after Clemens in the first place. Former federal prosecutor David Debold says the government has likely already spent "multiple millions" of taxpayer dollars on the Clemens trials.

"When you have these big, high-profile cases and a jury doesn't convict or a jury throws it out for some reason, it really raises questions about whether the government is putting its resources in the right location," Debold said.

Attorney General Eric Holder is standing behind the decision to prosecute Clemens twice.

"The charges are serious ones," Holder said Wednesday, adding, "It's about testifying falsely before Congress."  On that basis alone, Holder said, the prosecution is a "justified" use of resources.

The defense has asked Judge Walton, who is also presiding over the current trial, to throw out portions of Pettitte's testimony regarding his conversations with Clemens about HGH. As the umpire in this case, it will ultimately be Walton's call to make.

Fox News' Mike Levine contributed to this report.