The Arsenal forward complained of pain in the final warm-up before Sunday's victory over Stoke and was withdrawn from the starting line-up.
Arsene Wenger called the injury "a mystery" in the aftermath of the game but, according to the Arsenal website, further examination has revealed "slight damage to his posterior abdominal wall".
Walcott has been ruled out of Arsenal's next four games - trips to West Brom in the Capital One Cup and the Premier League, a league game at Swansea and Napoli's Champions League visit.
And he will be unavailable for England's closing Group H qualifiers against Poland and Montenegro - a Wembley double-header which will determine whether Roy Hodgson's side qualify for Brazil, go into the play-offs or miss out altogether.
Wenger said: "Theo will be out for a few weeks. He has developed some damage to his posterior abdominal wall. It's not a hernia, but it's a little structural problem in his abdomen.
"He will have the procedure in Germany on Wednesday and, because it's so minor, we can begin his rehab immediately.
"We are pleased it's being dealt with quickly and he shouldn't miss too many Arsenal matches. But he will miss the forthcoming international matches with England."
Walcott started both England's September qualifiers, a 4-0 win against Moldova and a goalless draw in Ukraine.