The Manchester United skipper attempted his comeback in pre-season after snapping his ligaments in Basle last December. But just four games into the Premier League campaign, the Serbian has been forced to go under the knife again for further surgery that will keep him out for two more months.
It is a grievous blow to United, who are already without Chris Smalling and Phil Jones and are left with just two fit senior central defenders, but Ferguson is not entirely surprised at the turn of events and he said: "I don't think he was ever 100%. I noticed a couple of times in training that he was limping a little bit. Then he started feeling tightness in his knee."
He added: "He wanted to carry on and in that situation that is what tough guys can do.
"Obviously the main operation was to correct the cruciate but when you do cruciates there is always the danger that the cartilage or meniscus is damaged also and that was the case."
It means Rio Ferdinand will partner Jonny Evans against Tottenham at Old Trafford this evening, with Birkenhead-born rookie Scott Wootton acting as cover.
Under the circumstances, it is understandable why Ferguson might hope Roy Hodgson does not call Ferdinand back into the England fold when he unveils his squad for the World Cup qualifiers with San Marino and Poland next Thursday.
At least United have an unbeaten home record against Tottenham that dates back to 1989 to comfort them. And there is also the potential for Wayne Rooney starting alongside Robin van Persie for the first time, even if Ferguson insists he does not know what his best strike partnership is going to be.
"It is early doors but at the moment I don't know where I am going in the sense of what my best partnership will be," said Ferguson. "Probably the strongest part of the club will be in the striker department. It (Van Persie's arrival) should give everyone a push."
"Danny Welbeck is in the same position as Javier in that they are not the first-team choices at the moment. That doesn't mean to say it will stay that way because competition is always healthy and them being the kind of young lads they are will be desperate to establish themselves."