The 29-year-old, who has made just two La Liga appearances in his two seasons at Camp Nou, featured heavily in Barcelona's pre-season matches, starting all three of the club's International Champions Cup games.
Barcelona paid Ajax €13 million for Cillessen in August 2016, but Marc-Andre ter Stegen remains the club's first choice. However, the Netherlands international has been reported as a target for Manchester City as they are looking for a goalkeeper to step in for Claudio Bravo, who could miss the rest of the season with an Achilles injury.
But Cillessen has picked up his own muscle problem in the early stages of the campaign and the Catalan side are unsure when he will return.
A statement on the club's official website said: "Barcelona goalkeeper Jasper Cillessen has picked up a sprain to an intercostal muscle on his left side.
"His availability for the upcoming fixtures will depend on his recovery from the injury."
Meanwhile, midfielder Sergi Samper was diagnosed with a sprained ankle and missed training as the Blaugrauna prepared for their second league game of the season.