Tipuric has played the full 80 minutes in all three of the Ospreys' RaboDirect PRO12 games over the past month but Gatland has revealed that the long-term prognosis may mean the 24-year-old isn't available in June.
"Justin has a shoulder problem which might need some work doing at the end of the season," said Gatland. "It could need an operation, a shaving of some bone, and there's a possibility he could be ruled out of the tour by it."
Wales are already without skipper Sam Warburton for the trip south after the Lions captain dislocated his shoulder at the end of the RBS 6 Nations win over Scotland last month.
Gatland is confident there is enough strength in depth in the back row to succeed this summer, though, and he says that losing Tipuric would not necessarily prompt him to pick another specialist No7 for the Test matches in Durban and Nelspruit.
"We've got other options because I think South Africa is a team you can play against, because of the size of the players they pick in their back row, without a specialist openside," added Gatland, with the Boks likely to employ Duane Vermeulen, Willem Alberts and Francois Louw at the back of their formidable pack.
"We could shift Dan (Lydiate) from blindside to openside and bring in Bradley (Davies) at number six to deal with Alberts. It's certainly something we are exploring."