Lloris moved from Lyon to White Hart Lane on transfer deadline day but has only made one Premier League appearance as Brad Friedel keeps him out of the side.
While Deschamps insists Lloris, who saved a penalty against Spain in their recent World Cup qualifier, will continue to be his No.1 choice for France, he questioned why he moved to Spurs without first speaking to Villas-Boas and gaining an assurance he would be first-choice.
He said: "His situation appears to me to be incomprehensible.
"We are not talking about a young goalkeeper but a guy who has been the France keeper for several years, who has played dozens of matches in the Champions League.
"The problem is that he jumped on the train when it had already left the station and he did not start the season.
"The English league had started when he signed in August. The really important thing is that a player speaks directly with his coach and if Hugo had done that, maybe he would not have signed for Tottenham.
"But as for the French team, he is not in danger. He proved against Spain that he is a great keeper."