Adebayor had initially refused to play in the African Nations Cup due to a row over team security and unpaid bonuses, but following talks with the country's president the Tottenham striker now has his heart set on taking part in the tournament.
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."
Villas-Boas has always insisted when asked about the situation that he would be happy to let Adebayor go to the tournament despite the fact that it would leave him with only one recognised striker in Jermain Defoe.
Togo head coach Didier Six must submit his squad for the cup by midnight and Adebayor is keen to be on it despite initial fears he had raised over the team being subjected to a similar attack to the one that took place in 2010 in Angola.
Three people, including Togo's assistant coach, were killed when terrorists ambushed the team's coach. Adebayor hid under a seat and survived the attack.
Togo's president Faure Gnassingbe appears to have allayed Adebayor's fears about another attack on the team later this month.
"I have met the head of state on two occasions. We talked, I told him what was wrong with Togolese football," Adebayor said. "He must, at all costs, find solutions. We discussed it and he guaranteed that he will take charge of everything.
"If you ask me the question of whether I will go to the African Nations Cup, it is still 'yes and no' because I have a club. I have to go and announce to them the decision that I have taken, and then I will return to the national team."