Pettitte acknowledged Thursday the new investigation might mean he'll be interviewed again by federal officials.
"I'm just prepared that it might happen," Pettitte said before a workout at Legends Field. "There's nothing I can do. Until somebody tells me to go somewhere, I can't do anything."
Pettitte is in the middle of a dispute between ex-teammate Clemens and Brian McNamee, the former trainer of the two pitchers. Pettitte has told congressional lawyers that Clemens informed him nearly a decade ago that he used human growth hormone.
On Wednesday, the House Oversight and Government Reform Committee sent a letter to Attorney General Michael Mukasey asking the Justice Department to investigate whether Clemens committed perjury or made knowingly false statements to the committee during its investigation into performance-enhancing drugs.
Pettitte's testimony, among others, was cited in the letter to Mukasey. Pettitte said he is uncomfortable with the situation.
"It makes it extremely difficult," he said. "I don't like any of this. I cannot stand it. I told you how I feel about him. I hate it. It's like a part of my family that's going to have to go through this. It's a bad deal."
Clemens has denied using performance-enhancing drugs and said Pettitte "misremembers" the conversation.
Pettitte hasn't talked with his lawyers about the possibility of being interviewed again.
"It doesn't take a whole lot to figure out what's going on," Pettitte said. "I think that's a long process down the road if that's ever going to come up."
After throwing batting practice earlier this week, the left-hander received a loud ovation from fans.
"I've definitely noticed it, and obviously it makes you feel good," Pettitte said. "I appreciate the support. They've been great. Of course, it makes you feel good to hear people cheer for you.
"I don't feel like I'm some kind of hero in this thing at all. I've made some mistakes, and I've admitted to them. However people want to handle that, that's how they handle it. I can't change everybody's opinion or what they're going to think of me and how they're going feel about me."
Pettitte admitted using HGH in 2002 and 2004.
"I know what I have to do," Pettitte said. "The commitment I made to this organization. I know what I have to deal with. Anything that comes up in your life is a distraction. You go with it, and you go out there and do your job the best you can. That's what I've always done and that's what I'll continue to do."
Yankees manager Joe Girardi said a wait-and-see approach is the best way to handle the situation.
"You take it as it comes," Girardi said. "To try and make a prediction of what's exactly going to happen, none of us knows. So you take it as it comes and deal with it."
Girardi doesn't plan on talking more often with Pettitte because of the investigation and its possible distraction.
"With Andy, you pretty much know how he's doing," Girardi said.