The Scotland striker's absence is a serious blow for his Everton manager, Joe Royle, who is attempting to pull his side away from the foot of the Premiership table. Ferguson's injury is also bad news for the Scotland coach, Craig Brown, as the 24-year-old striker could also miss three World Cup qualifiers.
Ferguson is now ruled out of the games in Latvia and Estonia on 5 and 9 October, and could be struggling to make the home match with Sweden on 10 November.
Ferguson played outstanding football in the first two games of the Premiership, against Newcastle on the opening day and against Manchester United four days later when he netted twice.
However, he has been struggling for a few weeks with the knee and on Tuesday went into hospital for exploratory surgery. A cartilage operation followed.
Among the Premiership games he will miss is the Merseyside derby on 20 October at Anfield. Ferguson would have missed the next couple of matches, though, after being sent off against Blackburn Rovers last Saturday.
Royle might now be forced into looking for a replacement as Everton attempt to end a run of eight games without a win when they play Sheffield Wednesday on Saturday. Wimbledon's unsettled striker Dean Holdsworth, rated at pounds 4m, is understood to be the top target.
Royle is desperately seeking a victory on Saturday to try and appease the fans after the Coca-Cola Cup defeat by Second Division York on Tuesday night. But he insisted: "This is no time to panic. We do need some new faces and we are constantly asking about players who I know would improve us.
"But the players I want are not available at the moment. I am not going to give false hope of making a signing today or tomorrow. It is a question of waiting. The players are very low. They are frustrated and know they are letting themselves and the supporters down at the moment.
"But I am confident in the players that we have here and that things will come round. We have had two seasons of immense progress and that does not suddenly turn into a situation of panic. We need everyone to stand up and be counted but at the moment one or two are going missing."
Royle added: "The game against York should have been out of sight at Goodison Park. It should have been academic but it wasn't. Overall we got a hiding. I was very disappointed. Certainly going out of the cup at this stage wasn't in the script as far as I was concerned."
Glenn Hoddle is set to reap the benefit of England's Euro 96 heroics when England meet Poland in a World Cup qualifier next month.
Wembley is on the way to becoming a 76,000 sell-out for the 9 October game, with more than half the tickets already snapped up by fans wanting to see Hoddle's first game at the twin towers since he was installed as Terry Venables' coaching successor.
"We haven't seen interest like this for a very long time," a Wembley spokesman said.
Wembley expect another rush for tickets today when Hoddle names his squad for a meeting with opponents who have stood between England and World Cup success on many occasions down the years.
The stadium spokesman added: "There is always an increase in demand for tickets after squads are announced, so we would advise people to book now to avoid disappointment."
Hoddle's men kicked off their Group Two campaign with a 3-0 win in Moldova earlier this month as they look to book their place in the 1998 finals in France.Reuse content