Owen pulled up during Sunday's League Cup final against Aston Villa, having scored United's equaliser in the 2-1 win.
"It's a terrible blow for the lad," Ferguson told reporters. "It's more serious than we thought.
"He never missed a training session all season. The heavy pitch at Wembley played some part, but it's also bad luck."
Owen, who has scored nine goals in 31 appearances for United since joining on a free transfer from Newcastle United last year, will undergo surgery on Monday.
In-form Wayne Rooney is also a worry for Ferguson after playing nearly the whole game in England's friendly against Egypt at Wembley on Wednesday and defender Jonny Evans will miss Saturday's Premier League visit to Wolverhampton Wanderers.
"We have to assess Wayne because he played almost 90 minutes for England the other night at Wembley, which I was disappointed in," Ferguson said.
"When you're playing on that pitch for almost an hour on Sunday and then nearly a full game on Wednesday, it's far too much. He's a doubt.
"It's disappointing as there were some changes made and I thought Rooney would be one of them, especially as he already had a slight injury from Sunday."
With Owen ruled out Ferguson's striking options are thin with Rooney and Dimitar Berbatov his only experienced forwards as the season reaches its climax.
However, there was better news on Rio Ferdinand who will return to partner Nemanja Vidic in central defence at Wolves.
"Rio is back which is good news," Ferguson said. "It comes at a good time with a big game against Milan next Wednesday.
"Having the Ferdinand-Vidic partnership is a big boost in terms of the experience and consistency they've shown over the last few years. That will be important to us in the run-in."
England midfielder Owen Hargreaves is also close to a return and has been scheduled to play for the reserves on Thursday.
Hargreaves has not played since September 2008 because of tendonitis in both knees.
"We've pencilled him in for a reserve game next Thursday and he's been training with the first team, which has been good to see," Ferguson said.
Follow FFT.com on Twitter
Join FFT.com on Facebook
