Villas-Boas confirmed the club had taken action against Modric who resumed training on Monday while the first team are on tour in the United States.
Modric has been fined £80,000 for missing training amid speculation of a move away, with Real Madrid thought to be the favourites for the midfielder's signature.
A statement on the club's official website on Monday night read: "The club can confirm Luka Modric has returned to training today at Spurs Lodge. The coaching staff will now determine the remainder of his pre-season preparation."
Modric has stated his desire to leave the north London club this summer, having remained faithful to them last season after widespread interest - including from Chelsea, then managed by current Spurs boss Villas-Boas.
Tottenham are willing to sell Modric at the right price, but Press Association Sport understands they are looking for a fee nearer to £40million than the widely-reported figure of £35million. Manchester United and Paris St Germain are also reported to be interested in the 26-year-old.
Villas-Boas said at a news conference in America: "Hopefully the situation does not drag on because it doesn't help Luka and it doesn't help to solve in any way the situation. The situation is not dependent on Tottenham, it is dependent on the clubs who are interested in the player.
"It's the first time Luka has taken these actions. The chairman and myself have been very open with the situation by saying we are willing to listen to offers for the player, which is uncommon. He has had many (expressions of) interest in the past, like last year, but he has always behaved professionally.
"We never doubt his human qualities but the club has to take action regarding a player who is missing on club duty and that's what we are doing. We have to hold on to our values and our rights and at the moment, the situation for Luka is that he is under club discipline."
The Portuguese, who was speaking before Modric's return to training was confirmed, added: "The player's behaviour at the moment is not what we want and that's why we are trying to bring him back to Tottenham duties. The last I heard he was back in London. Unfortunately for him he is going to have to be fined by the club for not being present.
"He is a player who has offered so much to Tottenham so we have to have a sense of respect for what he has done over the years for us, but the chairman feels that the fact he is not present is not common professional behaviour."