The 22-year-old faces at least six weeks on the sidelines after tests showed he had sustained a hairline fracture in his left foot following a hefty tackle from Liverpool defender Daniel Agger early in Wednesday night's friendly against Denmark at Wembley.
Wilshere played on following treatment until he was replaced on the hour, and afterwards maintained it was "just a bruise" when he spoke to reporters, having been initially assessed by the Football Association.
It is understood the fracture was so minuscule that the scanning equipment within Wembley failed to detect the issue following a precautionary examination by England's medical staff, and it was only when Arsenal, via an independent radiologist, conducted a more detailed test of the injured area that the real problem became more apparent.
Although Wilshere's place in the World Cup squad - a provisional 30-man party set to be named on May 13 - does not look initially in any serious jeopardy, the midfielder is nevertheless now set to miss at least eight club fixtures - starting with Saturday's FA Cup quarter-final against Everton and then next week's second leg of the Champions League last-16 tie away to Bayern Munich.
Wenger said at a press conference on Friday morning: "I believe it (tackle) was accidental. Jack will be out for six weeks.
"It is a blow for him and for us, from now on we want to get him to recover and come back as quickly as possible and prepare for next season.
"You can only be very down, especially in the first days.
"He is in a boot and has gone away for a few days to get away from things and think about something else."
Arsenal remain positive Wilshere will be able to return to play some part in the final few matches - unlike forward Theo Walcott, whose own World Cup dream was shattered by a serious knee injury in January.
Although it will be of little comfort, Arsenal will be compensated financially for the injury and the Barclays Premier League club will not have to pay for the midfielder's wages - reported at around some £100,000-per-week - while he is sidelined, with the money coming from the FA's insurers.
Wenger maintains there was no pre-agreement over how long Wilshere could be played, or how the injury was managed by England.
"At some stage it is the player who gives you the indication, you trust always the player," the Arsenal manager said.
"Sometimes you give him a few minutes to tell you how he feels and if he has pain, we cannot make an instant decision with an X-ray, so it is the player who tells you if he can go on or not."