And Richard Dunne was reportedly involved in a training-ground row after being dropped at the weekend.
But Houllier said: "I've read about dissent in the squad over training methods but it is not true."
"I know it is different to what it was before but it is not true and the players will adapt gradually.
"We do a lot of work with the ball, we play a lot of games, we do some tactics as well.
"Do people have to adapt to a new manager and methods? In a way, yes. You adapt or you die. We are changing a lot of things and that upsets the comfort of some players.
Give your reaction to Houllier's comments
"I am not going to talk about the players who are dissenting and not happy. Any manager who runs a team knows the players who are playing are happy, and the players who are not playing are not happy.
"They think the methods are not good and they think the manager is not the right person but we have to live with that.
"We know that we are changing things, we know that sometimes people are whingeing and moaning but they have a fantastic job.
"They are paid high wages to play and enjoy football. This is a fantastic job and sometimes you forget that."
The 63-year-old Frenchman has had a difficult time since
taking over at Villa Park
in September following Martin O'Neill's
shock resignation
in August.
His side have struggled for results, a
2-1 victory over West Brom
on Sunday halting a run of three league defeats, while Houllier was forced to
clarify comments
which angered fans following the
3-0 defeat
by his former club Liverpool.
And it was reported during the week that
Dunne reacted angrily
to being dropped for the West Brom game and being stripped of the club captaincy.
I had a lot of players who either had not played for a long time or needed a game
Gerard Houllier
But Houllier said: "There was not an incident with Richard Dunne. Not at all. I took a football decision not to play him and [Carlos] Cuellar came in and did extremely well and he will be playing
against Wigan
[on Saturday]."
And Houllier insisted that playing some of his out-of-favour senior players in a behind-closed-doors friendly with Leicester was not a punishment but was intended to help them maintain match fitness.
"It is not a punishment when you play a behind-closed-doors game to help players keep their fitness," he added.
"It is a punishment when you don't play at all, when you are left out, but I had a lot of players who either had not played for a long time or needed a game to restart like Nigel Reo-Coker.
"We wanted to have that game. We would probably have done it a week or two earlier but because of the snow we couldn't do it so it was an ideal opportunity to have it with Leicester.
"Robert Pires, John Carew, Nathan Delfouneso, Stephen Ireland; all those not involved for a long time played that game. Some we gave 70-80 minutes, others played the full game.
"It was just an ideal means of training and keeping the match fitness because the problem is the reserves don't have many games and, because of the weather, a lot of games have been called off."
Source: BBC Sport
Source: BBC Sport