Fati was forced off in the first half of the Seagulls' 3-2 win away against Nottingham Forest in the Premier League two weeks ago.
De Zerbi initially stated that the 21-year-old is facing "a long time" on the sidelines along with Tariq Lamptey, who also picked up a muscle problem in the victory at Forest.
Recent reports have hinted that Fati has made progress in his recovery from injury, but De Zerbi has since suggested that the Spaniard will not be available for selection any time soon along with Danny Welbeck and Julio Enciso who are still recovering from respective muscle and knee issues.
Speaking at a press conference on Friday ahead of Brighton's encounter with Burnley on Saturday, De Zerbi said: "The news about Ansu Fati is, I think he needs three months from the day of the injury.
"It's bad news for us because he was playing better, he was understanding better the idea.
"I'm sorry for him, I'm sorry for the team, especially now when Welbeck is not playing, Enciso is not playing."
Fati, who has chipped in with four goals and one assist in 12 starts for Brighton since joining on loan from Barcelona, is set to miss the next nine matches across all competitions.
Brighton are also having to cope without long-term absentees Solly March (knee) and Pervis Estupinan (muscle), while Adam Webster and Facundo Buonanotte have both been ruled out of Saturday's game due to unspecified problems.
However, De Zerbi is able to call upon both Lewis Dunk and Mahmoud Dahoud who have both served respective two and three-match suspensions.
"Webster is still unavailable to play. I don't know when he will play," said De Zerbi. "But it's important for us that Dunk and Mo (Dahoud) are available because they're both very important, especially in this moment.
"We are going through a difficult moment in terms of injuries and having two players available is important."
Midfielder Adam Lallana is also in contention to feature after missing the 2-1 victory over Brentford on Wednesday.
Discussing Saturday's opponents Burnley, De Zerbi said: "They have a clear idea, a clear style, I think they deserve more points.
"But it is still difficult for a small club when you win the Championship, the first year in the Premier League with young players and new players for the league is difficult."
Brighton currently sit eighth in the Premier League table and just two points behind Tottenham Hotspur in fifth, while Burnley are still in the relegation zone and are three points adrift of safety.