The forward is yet to decide whether he will travel to South Africa for next month's tournament and has been left out of Togo's squad for the warm-up match against Oman.
A dispute with his national federation is also clouding the issue, but the 28-year-old's main concern is whether or not security can be guaranteed.
Adebayor has bad memories of the Africa Cup of Nations after being part of the Togo squad whose team coach came under gunfire as it crossed the DR Congo-Angola border ahead of the 2010 tournament.
The attack claimed the lives of two Togolese officials and an Angolan bus driver, and also left many in the Togo squad mentally scarred.
Villas-Boas said: "It's very difficult for me to tell [whether Adebayor will travel]. 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 that 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."
Adebayor has denied that is dispute with the Togo federation is over bonuses.
The 2013 Africa Cup of Nations will take place from January 19 to February 10.