Lloris signed from Lyon for £8 million on transfer deadline day, but he has only started one Premier League game so far, with Villas-Boas preferring to use the Frenchman in the Europa League.
The Tottenham manager has opted to stick with 41-year-old Brad Friedel in the club's biggest games - a decision that has angered France head coach Didier Deschamps, who decided to stick with Lloris as his captain following his appointment after Euro 2012.
Lloris has brushed off speculation that he is unhappy at playing second fiddle to Friedel in the past, but he suggested on Thursday that he is not content with the Tottenham manager's rotation system.
"I'm training, I do the maximum, and the coach made his choice," Lloris told L'Equipe after France's 2-1 win over Italy.
"It is difficult to accept. It is a little hard. You will have to ask the coach. I just stay professional."