Capello is due to meet FA chairman David Bernstein later this week to try to bring some stability to a situation that had already led to calls for the England coach to be axed following his controversial comments about the John Terry saga.
"There's nothing wrong with having an opinion," said Ferguson.
"I think what will happen in the next few days is there'll have to be a coming together of the FA hierarchy and Fabio Capello because he's the team manager, he has the importance of that position. Without question the most important person at a football club is the manager."
After expressing his displeasure during an interview with Italian state broadcaster Rai 1 on Sunday evening, Capello was tight-lipped at Anfield on Monday night. He claimed "I can't talk" about the furore when quizzed and the Italian also rejected an opportunity to confirm whether he would be staying in his job, even if his mere presence on Merseyside was a positive indication.
And Sports Minister Hugh Robertson has come out and backed the FA, no matter what the consequences. Robertson told Sky Sports News: "The FA had a difficult decision to make. The chairman spoke to his board, I think weighed it all up and took, in my view, exactly the right decision.
"If the consequence of that is the manager walks away, the consequence of that is John Terry walks away, I would regret both of those two things enormously, but so be it. The FA have acted very sensibly, very reasonably, and they have come to the right decision. There were really two things they have to tackle at the end of last week.
"There was the moral case, which was a very difficult one because in this country you are innocent until you are proven guilty, so it would have been very tough to take action on that front.
"There was also the practical side of it which makes it extraordinarily difficult for John Terry, fabulous footballer and a great captain though he is, to discharge that responsibility in the white heat of this kind of publicity during the European Championship."
Terry has been charged with racially abusing Anton Ferdinand, a charge he denies.