Real Madrid have been heavily linked with the Croatia international this summer but Spurs have not been prepared to compromise on their asking price.
Villas-Boas believes that Modric must accept that there is little the club can do if an agreement is not reached before the end of the transfer window.
"He has been training separately," the Portuguese told Sky Sports. "Now it is important for Luka to feel mentally ready to come back to first team training
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"These boys are at a different level in terms of their preparation, concentration and commitment.
"I think the player has to understand that the club cannot do anything about other clubs' offers.
"We have a value and an interest that we have to defend, and we are waiting to reintegrate the player if the offer is not matched."
Modric's future at White Hart Lane is in doubt for the second consecutive summer, with Villas-Boas himself pursuing the playmaker this time last year as manager of Chelsea.
The 34-year-old hoped a resolution would be reached as soon as possible, ideally with Modric returning to the first team.
"We will try to solve it as soon as possible," he said. "It is the second time we have been through this situation.
"It is obviously difficult for him, but the chairman is defending the club's interests and the player has to understand that, and the fact that the offer does not meet the chairman's demands means we can't do anything.
"The player is a good professional and hopefully he will return to the team."
When asked if Modric could be ready to play at the start of the season, Villas-Boas replied: "Obviously he will have to raise his fitness level, and the sooner that we can have him reintegrated mentally and then physically, we will then see how things go."