The 22-year-old player, whose energy and distribution skills allowed him to break into the first team this season, picked up the injury during last month's 1-0 win at Everton.
"It's unfortunate, it's worse than we thought," Ferguson told a news conference.
"We did further scans... we're going to have to give him a break till maybe Christmas time."
Cleverley's return was not the only date on Ferguson's mind as his second-placed side seek to make up ground on Premier League leaders Manchester City by the start of the new year, starting with Saturday's trip to Swansea City.
"By January 1 we hope we'll be in the right position in the league, which is always an important time for me," said Ferguson, whose side trail their neighbours by five points after 11 games.
"It's always crucial in my diary and calendar that we get there."
His mission will be helped by the return of winger Ashley Young, who has recovered from a toe injury and will be fit for this weekend's match.
Despite Cleverley's longer-than-expected recovery time, Ferguson was confident he had plenty of midfield options and backed England manager Fabio Capello's confidence in teenage defender Phil Jones's ability to play a centre-of-the-park role.
INFLUENTIAL PLAYER
The Scot deployed the 19-year-old in midfield against Liverpool earlier this season, while Capello did the same thing in this month's international friendlies against Sweden and Spain and likened Jones to former Italy great Franco Baresi.
"Since he's joined us his improvement has been really eye-catching in the sense that we know he's 19 years of age, we know it's a big step up from Blackburn to Manchester United," Ferguson said of his close-season signing.
"He's been fantastic, he can play anywhere. He's versatile, he's two-footed, he's quick, he's got good perception of the game so I'm not surprised at what Fabio is saying.
"I think he can be a really influential player for us and England in the next few years."
Ferguson has not been afraid to make some bold selections this season when injuries have hit, even selecting striker Wayne Rooney in the centre of midfield where he excelled against Otelul Galati in the Champions League this month.
However, he pointed out that with Michael Carrick fit, as well as Darren Fletcher, Ryan Giggs and Park Ji-sung, he was not short of options involving players more used to the territory.
Defender Chris Smalling will miss the game in Wales but may return for Tuesday's Champions League match at home to Benfica, while striker Danny Welbeck is still recovering from a muscle strain sustained on international duty with England.
Champions United are second in the table with 26 points and Ferguson was expecting a tough encounter with fearless Swansea.
"I think everybody has been taken by Swansea, the way they have played," he said. "They have kept their philosophy of playing attacking football."
