The nation's governing body announced the move on Friday following confirmation that Terry, who has been charged with racially abusing QPR defender Anton Ferdinand, will not stand trial until July 9.
That date is after this summer's Euro 2012 finals and England coach Fabio Capello has previously stated his intention to keep selecting Terry until the conclusion of the case so the Chelsea defender is free to play in Poland and Ukraine.
However, the FA board has now relieved Terry of the captain's armband as they feel it would be wrong for him to lead England into the European Championship with such a serious accusation hanging over him.
Mills played alongside Terry for England, winning 19 caps, and the ex-Leeds and Manchester City right-back is dismayed by the decision and reckons it sends out mixed messages.
"I'm very, very surprised," he told Sky Sports News Radio. "I don't quite understand what this does.
"For me, it had to be all or nothing. If John Terry is not suitable to represent his country as captain, then why is he suitable to represent his country at all?
"For me, there is no differential between the captain and the rest of the team. I represented my country and I certainly didn't feel beneath the captain, and I certainly didn't feel I could get away with stuff the captain would be able to get away with.
"I think you should all be treated as one, I think it's a bit of a halfway house, and also, whatever happened to being innocent until proven guilty?
"If John Terry is proven guilty in a court of law, then of course, he deserves every punishment he gets. But the law in this country states, you are innocent until proven guilty."
The Crown Prosecution Service (CPS) announced just before Christmas that Terry would be charged and Mills believes that if the FA was going to act, that was the time to do it.
Instead it has acted after the trial date has been set, a date which Mills believes could have done the FA a favour.
"The timing of the trial is somewhat bizarre," he said. "I do actually believe that suits England, the fact he can go and play for England in the Euro 2012 Championship.
"On the back of that, he may well decide to retire from international football and that may take away a lot of the question marks to be answered by the FA if - and it's a big if at the moment - John Terry is found guilty.
"I don't quite understand why this decision has suddenly been taken now. John Terry was charged with this several weeks ago. Apart from a date of a trial being announced, nothing has changed.
"I find it a little bit bizarre and also, it's a little bit of a cop-out from the FA. They're trying to appease certain people, possibly in the media.
"I don't understand why you cannot represent your country as captain because you've been charged with an incident, but you're still available to represent your country.
"I don't think either decision is correct at this moment in time, I think you have to stick by the law in this country that you're innocent until proven."
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