"It's sad for Ousmane and for Desire of course, because of their injuries, and we're losing two important players for tomorrow's match," Deschamps told reporters on Monday.
"But we did things in a professional and progressive way, as we always do with all the players, taking into account their own feelings."
PSG reacted angrily after Dembele sustained a hamstring problem and Doue injured his calf during Friday's 2-0 win over Ukraine in World Cup qualifying, accusing the French Football Federation (FFF) of ignoring medical warnings and describing the injuries as "serious and avoidable".
The Ligue 1 champions said they had submitted medical information before the training camp began and called for a more transparent protocol with the FFF to protect players in the future.
Deschamps pushed back against suggestions of conflict between club and country.
"This concerns two PSG players," he said. "But PSG are not our opponent - clubs have never been. I've been on the other side of that fence myself. Our only opponent is Iceland, and that's tomorrow."
Dembele is expected to be sidelined for around six weeks, while Doue faces about four weeks out. Both will miss PSG's Champions League opener against Atalanta later this month.