The 25-year-old defender had surgery on a long-standing knee problem this summer, but the injury continued to give him trouble after games.
"While Ledley King didn't suffer any reaction overnight to his knee, it has become clear that Ledley is not entirely comfortable," the Football Association's director of communications Adrian Bevington said.
"Therefore, as a precaution, the England medical staff and (manager) Steve McClaren felt it was in Ledley's best interests not to fly and so he is out of the game," he added in a statement posted on the their official site.
Despite the blow, McClaren can find some relief in the return of Manchester United defender Rio Ferdinand.
Ferdinand missed Saturday's goalless draw with Macedonia due to a back spasm, with King being deployed as a center defender.
"Rio has trained and it's good to have him back with us," McClaren said.
"He will be traveling with the squad and we expect him to train in Croatia, providing there's no reaction."
England are in charge of Group E of the qualifiers on seven points, leading second-place Israel on goal difference. Croatia are placed third with four points.