Thomas this week labelled the situation as "unfair" on the new boss ahead of his first World Cup qualifying campaign after the West Ham duo dropped out of the squad, but Coleman has been quick to protect his players by insisting that both players are injured.
Collison has been plagued by a series of knee injuries and it appears as if that may have flared up again, whilst new Hammers signing Collins, who hasn't played for the national side since March 2011, is suffering from a groin problem.
"I have seen Mickey's comments, he is paid to give his opinion but I don't agree," Coleman told reporters.
"Jack Collison has had a serious knee problem, not for six months or 12 months, but for two or three years.
"He has got through games when maybe he shouldn't have because he wants to play, and he has even come away with Wales when maybe he shouldn't have."
Collison in particular will have to be dealt with delicately given his past injury record, and Coleman is determined not to rush the midfielder back into action.
He added: "We know Jack very well, he has a lot of desire for football, he loves to come and play for Wales and we love having him play for Wales, but physically he cannot do it.
"He has not kicked a ball since the play-off final, where he ran himself into the ground and had a big impact. He has not done a lot since and he needs a rest.
"We left him out of the Mexico game as he had the play-off final coming up and he had played a lot of football, I think it was around 30 games for West Ham, and he is always trying to maintain his knee problem. Now he needs a complete rest.
"I will take some of the responsibility for naming him in the squad and then getting information on him.
"But if he is not right and he cannot play for West Ham, how can he play for us?"
Coleman also believes that it would be a risk to include Collins, but assured Welsh fans that the 28-year-old remains part of his plans.
He added: "James Collins, we think, has a hernia problem which may need surgery, he can't play. He limped off in a friendly in Portugal for West Ham so he can't play.
"They are two players who will always be in my thoughts and be there or thereabouts when I am naming my squad."