Grygera was nearing full fitness after playing a handful of games for the reserves, only to pick up a thigh problem a fortnight ago.
The 32-year-old faces another month on the sidelines, but boss Jol insists he could still stay at Craven Cottage if he proves his fitness.
"Grygera was very unfortunate," Jol told the Fulham Chronicle.
"He came back and was almost 90 per cent fit, trained with us and played with the reserves.
"But he had a setback and will be out for four or five weeks, and that's exactly what he didn't need because he was on the fringe of getting another contract with us for this season.
"The situation hasn't changed. He's here on a different basis because he's not under contract, but we will have to wait and see if he can come back."