The Togo international has been left out of the squad for a warm-up game against Oman, although he has denied reports his absence is down to a dispute over bonuses.
Villa-Boas confirmed after the 2-1 Barclays Premier League victory at Sunderland that there is a dispute between the player and his national federation but that Adebayor also has concerns over his safety.
Villas-Boas said: "It's very difficult for me to tell. At the moment there is a dispute between him and the federation, the player has spoken about it already.
"He has also said that situation is not just about the dispute that they have, it is also about the fact he doesn't feel comfort and safety in going to the African Nations Cup.
"I can't put myself in his position to tell if he is going or not going because I respect the player, I respect the competition and if he has to go we just have to make sure we address the problem he has."
The tournament starts in South Africa on January 19 but it is memories of the 2010 competition which still haunt Adebayor.
He was part of the Togo squad whose team coach came under gunfire as it crossed the border from the Democratic Republic of Congo into the Angolan enclave of Cabinda with two Togolese officials and an Angolan bus driver losing their lives.