Manchester United have suffered another serious setback in their defence of the Premier League title amid fears at Old Trafford that Darren Fletcher's career is on the line because of the health issues that have ruled him out for the season and left Sir Alex Ferguson with a gaping hole in his midfield.

Fletcher is taking what United have described as an "extended break" after doctors warned him he was putting his health at serious risk by continuing to play despite the rare bowel condition that has affected him for the last year.

United are so concerned about the health of the Scotland international captain they have been unable to put any timescale on how long he will need out of the game, or even guarantee that he will be able to resume his career.

Until now, the champions have attributed Fletcher's spells out of the team to a mystery virus, but the club have now disclosed they did this purely "to respect his right to medical confidentiality" and, with the player's consent, released more details in a statement that makes clear the seriousness of the issue.

"Darren has, in fact, been suffering from ulcerative colitis, a chronic inflammatory bowel condition, for some time preceding this [last year]," the statement said. "While he was able to maintain remission of symptoms for a considerable period, this has proved more difficult recently and Darren's continued desire to play and his loyalty to both his club and country has probably compromised the chances of optimising his health and fitness.

"He has therefore accepted medical advice to take an extended break from the demands of training and playing in order to afford himself the best chance possible of achieving full remission once again."

The news comes within a week of United's elimination from the Champions League coinciding with Nemanja Vidic rupturing his cruciate knee ligaments, an injury that will keep the club captain out for a minimum nine months. United do, however, have cover in the centre of defence whereas Fletcher's absence threatens to be a considerable blow given Ferguson's already significant problems in midfield.

Anderson has been ruled out until February with a knee problem, while Tom Cleverley will be missing until January with an ankle injury, and the club's failure to bring in the top-quality central midfielder that Ferguson wanted in the summer has led to Phil Jones and Wayne Rooney both being tried in the position.

United had tried, and failed, to sign Wesley Sneijder from Internazionale and Samir Nasri from Arsenal, and the club now have little option but to consider going into the January transfer market. Ferguson stated last Friday that he had "nothing in mind at the moment" but the issue is now so serious it is almost inconceivable that he will not at least look at potential targets.

Uppermost in Ferguson's thoughts, however, is the seriousness of Fletcher's condition and the feeling behind the scenes at Old Trafford that he needs to put his health first, whatever the ramifications for his employers. United rarely release public statements about player injuries or medical conditions and the fact they felt willing to break this policy is another demonstration of how grave their concerns are for a 27-year-old who should be at the peak of his game.

Fletcher, who has made 302 appearances for United and won 58 international caps, has looked noticeably gaunt at times and, in other moments, his face has appeared bloated because of the drugs he has been prescribed. He missed six months of action earlier this year but has always maintained before now that he did not know what the illness was. "I felt drained and weak and was bed-bound for a bit," he said in September. "The biggest thing was losing the weight. The virus was bad but for someone like me to lose the weight I did, it was really difficult to put back on."

United have gone public after a deterioration in his condition last week led to more medical tests. Fletcher was an unused substitute in the 2-1 defeat at Basel but had complained of feeling weak and was unable to train on Friday. "We request that his privacy is respected and hope that the removal of the additional stress associated with speculation regarding his health will also aid his recovery," United said.

Interview: What is ulcerative colitis?