Wright-Phillips has been sidelined since City's UEFA Cup quarter-final defeat by Hamburg and may need surgery, his club said on Friday.
"Shaun trained earlier in the week but he got a reaction so he'll have to see a specialist," City manager Mark Hughes said on the club's website.
"He's obviously not available at the weekend (against Bolton) and he may well have to have a wash-out of his knee in the close season. He needs to have it as soon as possible. That will enable him to start pre-season."
Middlesbrough's Stewart Downing is also out of the internationals after suffering a bad injury to his foot in last weekend's home match against Aston Villa.
England, who are top of World Cup qualifying group six with maximum points, play in Kazakhstan on June 6 with Andorra coming to Wembley four days later.
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