The striker was called up by Gareth Southgate this week for the match against Malta at Wembley on Friday and the trip to North Macedonia on Monday. Tottenham's James Maddison has also been forced to pull out as a result of the ankle injury that will rule him out until 2024.
Jude Bellingham also missed Real Madrid's LaLiga clash with Valencia on Saturday due to a shoulder problem.
"You’d be amazed at how complicated it is picking a squad," said Southgate on Thursday.
"All clubs are sensitive to information and you are trying to piece everything together. So, I couldn’t be certain that everybody in that squad will be there on Sunday night.
"Varying levels of doubt. Probably Callum Wilson is the biggest doubt. But equally, I am pretty confident the others can get through. They are all keen to be in the squad and that’s a really good sign."
Wilson suffered a hamstring injury in Newcastle's Champions League defeat against Borussia Dortmund in midweek and missed Saturday's 2-0 loss at Bournemouth.
Afterwards, Howe revealed Wilson faces a spell on the sidelines.
He said: "Callum won't travel with England. He's going to be out for a number of weeks."
Additional reporting from PA