This decision will leave Spurs without the Togo international for up to four games.
Villas-Boas has always insisted when asked about the situation that he would be happy to let Adebayor go to the tournament despite leaving the club short in the striking department.
Yet Adebayor hinted in an interview with africatopsports.com - published on the Togo Football Federation's website - that despite Villas-Boas' public declaration of support, the Portuguese may not be happy with the 28-year-old's participation in the tournament.
"That is what he said to the press, but not what he said to me," Adebayor said.
"There is a difference between what you say to the press and what you say in private."