"Duncan has had a long term bone problem in his foot which has recently flared up," said Wales physio Mark Davies.
"It is likely that he will now be in plaster for a period of time and we are currently taking specialist advice before predicting when he will be able to make a return, but we know he will not be available to us for our matches against the All Blacks and the Wallabies."
The news is a significant blow to the double Grand Slam winner who, with the length of his absence as yet unknown, now faces an even tougher task to force his way into Ian McGeechan's Lions squad for the 2009 summer tour.
Jones has been replaced in the Wales squad by John Yapp, while Tom James has taken the place of Gavin Henson who is suffering from an Achilles injury.
