The FA made the decision to remove the armband from Terry earlier today in a response to widespread calls for the 31-year-old to stand down.
Calls came as Terry, who has been charged with allegations of using racist language, would not stand trial until after Euro 2012 and the possibility arose that he could still be captaining England while the case was unresolved.
“I don't agree with it but you will have to ask the FA about it and the people responsible for the decision,” Sky Sports quote Andre Villas-Boas as saying when asked for his views on the decision.
“I think the statement from the FA is pretty clear on what was their decision-making and you will have to ask them the foundations of their decision.
Allegations were levelled at Terry after a heated encounter between Chelsea and QPR in October – Hoops defender Anton Ferdinand was the subject of the alleged racist abuse from Terry.
FA bosses claimed they had not acted sooner because they assumed the case would be heard a lot sooner and came to the decision so as to not have it hanging over the squad during their Euro 2012 campaign.
Villas-Boas was adamant that Terry’s role at Chelsea would not be affected in anyway by the situation and backed his captain to continue to put in quality displays.
“I don't think it will affect John's performances, not at all,” added the Portuguese when asked whether Terry’s form could be affected.
“From my opinion I don't agree with it [the FA decision]. John will continue to be our captain."
“It doesn't compromise on my decision-making. It obviously compromises the FA's decision-making and I am nobody to criticise what they decide.”