With Manchester United duo John O'Shea and Rafael both out for weeks, Ferguson, who was handed a five-match touchline ban by the FA on Wednesday for his referee rant at Chelsea, also revealed that he is now planning to push on for the Treble without Ferdinand.
Tough times: Rio Ferdinand (right) has been riddled with injuries this season
Ferdinand has been struggling with a back problem throughout the campaign, as well as the calf injury that has troubled him recently.
Ferguson has suggested Ferdinand could be facing a longer spell on the sidelines than had originally been envisaged when he suffered a calf injury in the warm-up ahead of United's surprise Premier League defeat at Wolves on February 5.
He said: 'Rio has been out for a few weeks now. We are not looking at this as a short-term situation.
Adding up: Rafael is carried off on a stretcher during the victory over Marseille on Tuesday
Crocked: John O'Shea
'He has not started training yet. We will be lucky to get him back for some part of the season.'
Ferguson is currently in the middle of a defensive crisis that has become even more problematic with the news that John O'Shea is out for five weeks with a hamstring injury, while Rafael will miss the next two to three weeks with a similar blow.
They were both substituted in Tuesday's victory over Marseille in the Champions League
Nemanja Vidic and Jonny Evans are also currently nursing problems, with Wes Brown and Chris Smalling are only the recognised centre-backs available for Saturday's Barclays Premioer League match against Bolton at Old Trafford.
'Vidic won't make it,' confirmed Ferguson. 'He is showing good recovery for this week and should be OK after the international break but not enough for Saturday.'
With only four fit defenders - Fabio, Smalling, Brown and Evra - it may force him to take a risk with the fitness of Northern Ireland international Evans.
He has not featured since standing in for Ferdinand against Wolves, after collecting an ankle injury in training shortly afterwards.
Ferguson added: 'It has been a bad spell for us. Only a few weeks ago we had every defender fit and things were looking great. It has all just fallen apart in the last week or so
'Hopefully Jonny Evans may be fit for Saturday, even if it is a bit of a risk. He has trained all week but he has been out for such a long time.'
Ferguson is hoping the forthcoming international fixtures will provide a break in a packed schedule that could come to United's aid.
Anderson is on the comeback trail, as is Owen Hargreaves, whose first-team action since September 2008 extends to a minute at Sunderland last season and five in this term's home encounter with Wolves in November when he limped off with a hamstring injury.
'Anderson is doing OK running-wise,' said Ferguson. 'He is getting closer. Owen Hargreaves has trained this week, which is good news. There are some promising things going to help us on the run-in.'
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Explore more:People: Alex Ferguson, Rio Ferdinand, Wes Brown, Nemanja Vidic, John O'Shea, Owen Hargreaves Places: Northern Ireland