The 29-year-old Australian, who picked up the problem during the 2-0 defeat at Birmingham on Boxing Day, was recovering well but has had to put his comeback on hold.
"Mark was progressing well, but he has suffered this unfortunate setback which has put his rehabilitation back another couple of weeks," said his manager, Steve McClaren. "The most important thing is making sure he is right and fully fit before he can resume first-team football."
Viduka, who has missed Boro's last nine games, had set his sights on the second leg of the club's Uefa Cup game against the Austrian side AK Graz on 24 February, but now faces a longer wait. Boro have won only three of their last nine outings, and only two of them in the Premiership, without the man recruited at a cost of pounds 4.5m during the summer to partner Jimmy Floyd Hasselbaink.