The striker fell awkwardly with 10 minutes remaining of the 4-1 victory against Watford at Stevenage Borough.
Head Coach Martin said early reports suggested Mounir had badly sprained his ankle.
"We are waiting for the results of a scan but I think he will be out for at least two weeks," said Martin this afternoon. "It's very disappointing news for Mounir because he'd been involved with the first team squad throughout pre-season."
Martin Jol expects Mounir El Hamdaoui to be sidelined for a couple of weeks after damaging his ankle on reserve duty on Monday night.