"Seeing him in Valencia is not impossible," Ducati sporting director Mauro Grassilli told Sky Sport Italia.
"Unfortunately, his injury is more serious than we initially expected.
"We have to see how his recovery goes, but there is a possibility that he will return in Valencia."
The Spaniard secured his seventh MotoGP title -- and his first since 2019 -- in Japan last month, but injured his right shoulder when he crashed on the first lap of the Indonesian Grand Prix on 5 October.
He suffered a fracture and injured ligaments and underwent surgery earlier this week.
Marquez had originally been ruled out of this month's Australia and Malaysia MotoGPs, with the Portugal and Valencia races completing the season in November.
The 32-year-old has a long history of injuries, including breaking his right arm at the start of the 2020 season, which almost forced him to retire.
Ducati has ruled out any connection between the two injuries.