The Springbok captain, who has missed much of the past year with groin and knee problems, sustained a fresh injury in training on Monday and was made unavailable for his Super Rugby franchise, the Johannesburg-based Lions, on the advice of an orthopaedic surgeon.
The Lions left for a four-game Australasia tour without Whitely and no date was given for the player's potential return to action.
"Warren Whiteley has not been medically cleared by the Lions Rugby Company medical team and will not join the Lions on tour until he is medically cleared," his team said in a brief statement on Thursday.
The potential absence of the number eight, along with lock Eben Etzebeth, will force the Springboks to select a new captain as they begin a new era under recently appointed coach Rassie Erasmus.
South Africa play Wales in Washington in June before three home tests against England.
(Reporting by Nick Said; Editing by David Goodman)
