Shanklin, whose first tour as a Lion was ended prematurely by injury four years ago, will be sidelined for around four months.
"I'm sure I can speak on behalf of the whole of Wales by offering our sympathies to Tom," said Blues chief executive Robert Norster, himself a former Lion.
"Tom and all our other Lions have given the very best for the Blues and it hardly seems fair.
"We're all feeling for him at this difficult time of disappointment and frustration."
Shanklin joins Tomas O'Leary in missing out on the tour itself having been named in Ian McGeechan's original 37-man squad, with the Munster scrum-half fracturing his ankle just days after the squad announcement.