"It doesn't look good. Gareth could be out for a long time. It looked like the Barnsley player took the ball first. There is no blame on him at all."
Whalley was felled by Chris Lumsden who was booked for the challange.
City started the second half without Daniel Gabbidon, the Wales defender suffered a back spasm that could, according to reports, see him miss the international teams trip to Azerbaijan.
Graham Kavanagh must also undergo treatment. City's skipper finished the game but was clattered by Mitch Ward and has taken a severe whack to his legs.
Whalley, Gabbidon and Kav injured at Barnsley
Gareth Whalley was stretchered off the Oakwell pitch just a few minutes after the second half started and despite doing the Ayatollah as he lay on his back with his leg supported it looks like he could have a serious injury. It's thought Whalley has medial ligament damage and Lennie told the Wales On Sunday