The England manager was reported as saying he would not pick Ferdinand again on a London Underground train.
He rejected this allegation, though he admitted he should not have discussed Ferdinand's position with members of the public.
"I'm disappointed that a story like that came out and I apologise to him," Hodgson told a press conference.
"Of course I didn't say that Rio's career was over.
"What I remember saying is talking to quite a lot of people on the tube, and one guy said, 'Is Rio in the next squad?', and I think I might have said 'I don't think so'. But I think that's about as far as I went.
"But I shouldn't say that of course. That's a mistake and I need to apologise for that.
"But this is one of the hazards I suppose of travelling on tube trains which is the best way for me to come into London - and then speaking to people on the tube train who ask me questions rather than sitting there tight-lipped refusing to ever open my mouth.
"I've paid for it. I shall learn in future, and maybe this will be a lesson for all those people who see me on the tube.
"Please don't be too offended if I refuse to answer any questions you ask me."
Ferdinand was left out of the England squad for the World Cup qualifiers against San Marino and Poland.
Instead Ryan Shawcross was called up to replace John Terry, who retired from international football days before the FA found him guilty of racially abusing Ferdinand's brother Anton.
Hodgson added: "I will apologise to (Rio Ferdinand) because there's no way I would ever indicate I wasn't going to use a player in that way," he said.
"But the thing is, I didn't choose him in the squad this time, and it's for the same reasons as before. We have other players, but certainly I'm not suggesting it's the end of the line.
"I would never dream of telling a player when its the end of the line or whatever I'm supposed to have said. That's up to the player to decide for himself, and hopefully that won't be the case.
"When I speak to him I'll make it clear I haven't selected him - who knows if I will select him in the next one - but it would be up to him whether he wants to be a part of it or not."
- Rio Ferdinand