The veteran defender has pulled out of the England squad and will be replaced by Tottenham's Steven Caulker.
The 34-year-old met with England manager Roy Hodgson in London on Sunday evening with both parties reaching an agreement that the center back's specific training and medical requirements could not be fulfilled during the international break.
Despite being unavailable for the World Cup 2014 qualifying fixtures against San Marino on Friday and against Montenegro next Tuesday, Ferdinand wants to continue playing for England.
"I'm disappointed Rio will not be available, but due to the detailed pre-planned training and medical program he must follow it's not possible," Hodgson told the FA's website. "However, I was pleased that Rio called and asked to meet with me. It was important to hear from him personally about the way he must manage his body between games.
"This is not to say he cannot play back-to-back games - he can and has proven so. He's out this time due to particular pre-planned details already in place for his program. I must place on record how I was impressed with his commitment to playing for England and I look forward to hopefully selecting him for squads in the future."
Manchester United manager Sir Alex Ferguson had previously revealed his concerns over Ferdinand's initial inclusion in Hodgson's squad, citing the defender's specific training regime tailored to contain a long-term back injury as a potential problem.
"It was important for me to be able to speak with Roy face to face and explain the situation, and one thing I made clear was that my passion and commitment to represent my country is as strong as ever," Ferdinand said.
"It is disappointing that I won't be able to play a part in the upcoming games but I told Roy that I want to continue to be available for England and I look forward to working with him in the future."
Tottenham defender Steven Caulker, who was originally named in England's Under-21 squad, has been promoted to the senior team following Ferdinand's withdrawal.