Carroll helped set up two goals in his first appearance for the Hammers since signing on loan from Liverpool, securing a 3-0 win over the Cottagers.
But he limped off after 68 minutes with a tight hamstring, and his absence was confirmed on the FA's official website.
"After picking up an injury in the match against Fulham, Carroll will not be part of the squad for England's opening Fifa World Cup qualifying matches next week," said a statement.
"Any decision on whether to call additional players into the squad will not be made until after the three fixtures on Sunday have been completed."
|ROAD TO THE WORLD CUP|
|12/1||England are 12/1 with Paddy Power to beat Moldova 4-0|
West Ham manager Sam Allardyce said the club were waiting to discover how long Carroll would be out of action for.
"He'll probably be on the treatment bench for a while. He over extended himself. We won't know the full extent of the injury until the scan and we see how serious it is," Allardyce told BBC Sport.
"We were ready to bring him off and unfortunately on that last jump he got hit and that twisted his body and pulled his hamstring by the looks of it.
"He is just so gutted because he has got injured and he can't go to England. That is why he is most disappointed, because he wanted to get off there.
The other strikers currently in the England squad for the fixtures against Moldova on September 7 and Ukraine on September 11 are Jermain Defoe, Daniel Sturridge and Danny Welbeck.