Thomas, the former St Kilda coach, said Harvey had failed to implement his playing traits on the winless Fremantle and suggested the former Bomber was "born to be an assistant".
Harvey said he didn't give Thomas' comments a lot of weight and despite heavy criticism following Fremantle's 0-2 start to 2009, the club remained galvanised.
"Grant should know better, than to draw analogies from afar," Harvey said on Wednesday.
"He's left the coaching scene and he's now making comments that you would have thought would have come from people in the media.
"What you have to realise is, where the club is at and what we're trying to do before you even make those sorts of comments."
Harvey refuted claims made by Thomas that "his charges don't respond to his coaching and don't play for him".
"We are galvanised, irrespective of what people want to write or say," Harvey said.
"The rapport with the players (and) the coaches is first rate considering where the group is at from an experience point of view."
Harvey acknowledged Fremantle was not playing as well as it should be and said the side's better players needed to do more.
Harvey said after a heavy turnover of players, depth would continue to be an issue.
"If you go and get 14 first year players, you don't go and get franchise players or you don't go and pinch players from other clubs, you're pretty much making a statement about where you're at and what you need to do," he said.
"We're trying as hard as we can to get the club up and running and we're doing as much as we can in and around the football club.
"Sure, we'd like to have had one or two victories by now, but it's a tough competition."
Harvey said there was too much external pressure on the football club and as a result the club was keeping its own expectations in-house.
He denied that after two losses Fremantle was in for its longest year to date.
"I don't want to take away the fascination of our year and how we may evolve," he said.
"Let's look at the positive side of it. Why do we always have to talk down about a couple of losses early in the year?
"Guys are getting more experience playing at AFL level, and the injection of some of our first gamers is important as we grow as a team."
Harvey said he would continue to select first-year players Stephen Hill and Nic Suban, while up to two more debutants may be selected for the clash with Adelaide this Sunday.
Development coach Steve Malaxos told fremantlefc.com.au Greg Broughton had been performing well in the WAFL and was ready for AFL football, while fellow rookie elevation Matt de Boer was probably one week away.
