Pires had not played any competitive football for seven months before joining Villa, but the 37-year-old instantly became involved and struggled to make an impact.
He was then left out of the side and questioned his lack of involvement and also feared Villa could be relegated.
But Houllier is adamant there is no problem between him and the former Arsenal star who played 65 minutes of Saturday's FA Cup win at Sheffield United.
Houllier said: "I think it (what he said) was taken out of context. He came to see me on Friday night. He said on the radio that he was happy not to play.
"I said `it's a good job that you are happy not to play because if a player is happy not to play, he doesn't deserve to be on the bench.' In fairness when he came here, I probably played him a bit too early. I admit that because it took him about three or four weeks to step up. Now he is getting better."
Source: PA
Source: PA