The flanker will now miss Wales' summer tour of South Africa after it was confirmed he will go under the knife this week.
The 25-year-old, who missed the third and final Test of last summer's Lions tour with injury as well, is not the only Wales and Lions star suffering with a shoulder complaint.
Warburton joins full-back Leigh Halfpenny - who had successful surgery on his shoulder last week - on the sidelines and both face a spell out.
"Following MRI scans and consultations with specialists, Warburton will have an operation and is expected to miss several months of action," said a Cardiff Blues statement.
"Everybody at Cardiff Blues wishes Sam and Leigh all the best during their rehabilitation."