The striker limped out of our 5-0 win over Burnley on Monday moments before the half-time break and looked in discomfort.
Guardiola says once the surgery is complete, the club's medical staff will have a clearer timescale on when the Argentine can return to action.
“Tomorrow we will do a surgery in Barcelona with Dr Cugat,” Pep said. “After that we don't know when he will come back and join us.
“After the surgery [we will know more]. He will tell us with more accuracy when he can come back.”
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He says with the schedule so packed, rotation will be key in ensuring his players are fit and fresh for the remainder of the campaign.
"We don’t have any doubts about Gabriel," he said.
"Only doubt we have is that not one single player with the preparation we had can play every game.
"No one player can play 90 minutes every three days. Raheem can play in this position, even Gundogan can.
"We have different options. Not a striker, but we have other options."
Meanwhile, John Stones is nearing a comeback.
The defender is yet to play since football’s resumption due to an ankle issue - but Guardiola says he is back on the training field and eyeing a return.
However, the boss hinted he won’t be ready to face Chelsea at Stamford Bridge on Thursday night as we look to make it three wins a row since the return of the Premier League.
"He is on the pitch training and getting better," he said. "Hopefully in the next few days he can play in the team."
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