Carlisle was hopeful that Dyke could turn the FA round following his appointment, but admits that he has brought "inevitable" criticism upon himself by naming the all-white lineup.
"My view of the FA is that a lot of their mechanisms have been terrible for many, many years. When Greg Dyke took the helm I was expecting, with all his experience at such a huge organisation like the BBC and the way that he oversaw change there, that he would be able to translate that into what they do at the FA," Carlisle told BBC Radio 5 Live.
"The biggest mistake I feel Greg Dyke made was announcing part of its constitution. If he was going to make sure there was representation on the commission, then surely he should have waited until he had the full line-up and then roll it out.
"Rolling out 80% of what the commission is and people only seeing Caucasian male faces will inevitably lead to this discussion."
Carlisle was replaced as PFA chairman last month, with Ritchie Humphreys being appointed his successor.