The team did not identify the area of concern but the Pittsburgh Tribune-Review said the Russian All-Star center is experiencing concussion symptoms, including severe headache and mild disorientation.
Penguins coach Dan Bylsma would not elaborate other than to say Malkin had been ruled out of Sunday's game with Tampa Bay.
"He's still being evaluated as to the extent of the hit and going into the boards hard," Bylsma told reporters.
"There's nothing to expect from this point ... We're waiting to see how he feels and reacts."
Malkin slid into the boards during the third period of Friday's 3-1 win over the Florida Panthers.
He was skating toward the Florida goal when he collided with Panthers defenseman Erik Gudbranson and fell onto his back before sliding hard into the end boards.
The Penguins' second-leading scorer remained on the ice while being attended, but eventually got to his feet and skated to the bench and went on to the locker room, not returning.
The talented Russian scored 50 goals and a league high 109 points last season after rehabilitating a knee injury in the off-season that cost him nearly half of the 2010-11 campaign.
With Malkin and fellow former league MVP Sidney Crosby, the Penguins had been made the favorites to win this year's Stanley Cup. They share the Atlantic Division points lead with the New Jersey Devils.