The 21-year-old appeared to twist his knee in the Royals' 1-0 victory over Colchester United in the League Cup.
Samuel, a reported target for Coventry City following a successful loan spell at the Ricoh Arena, is feared to have torn the cruciate ligament in his knee.
If that is the case then the youngster is likely to miss the remainder of the campaign, but Keen says that the club will wait for scan results before revealing the full extent of the damage.
"Hopefully it's nowhere near as bad as that," he is quoted as saying by GetReading.co.uk. "Fingers crossed he is OK. It's just too early to tell.
"He just felt something in his knee so we'll have it scanned and see where we go from there. It's a shame because he's been electric in pre-season and scored goals on loan at Coventry."
Samuel, capped three times for England at Under-19s level, has previously spent time on loan at Dagenham and Redbridge, Colchester United and most recently Coventry.