Roque, 18, was stretchered off injured in the first half of Thursday's 2-1 Brasileirao Serie A win over Internacional.
After further tests, Athletico decided that the player will not undergo surgery but a club source told ESPN Brasil that Roque will still be out for a minimum of three months.
With the Brazilian domestic season due to end in December, that may mean he has played his final match for the club.
Spanish champions Barça confirmed in July they had reached an agreement to sign Roque for an initial €30 million rising to a potential €61m based on performance-related add-ons.
The Catalan club's plan is to bring Roque to Europe in January, although a final decision will depend on the financial fair play situation with LaLiga at the time.
If Barça cannot afford to register Roque with LaLiga mid-season, there is a possibility the move will be finalised next summer instead.
In that scenario, he could yet play for Athletico again when the 2024 Brazilian season begins next April.
Roque joined Athletico from Cruzeiro in 2022 and has scored 27 goals in 77 appearances since, including 20 in 41 in the current campaign. He is the second top scorer in Brazil's top flight this season, with 11 goals.
ESPN's Adriana Garcia contributed to this report.