The Oman international has been used sparingly during the Barclays Premier League run-in as the Latics were relegated to the npower Championship.
It seems likely the custodian aggravated the injury in Wigan's 2-2 draw with Aston Villa in the final game of the season, his first match in eight, and he is to undergo an operation in order to be fit for the start of next season.
A spokesman for the former Bolton keeper said: "Ali Al Habsi, the Wigan and Omani international goalkeeper, has suffered a recurrence of the shoulder injury sustained earlier in the season.
"He will be undergoing surgery immediately on Wednesday to ensure his fitness for the start of next season and will therefore be unavailable for Oman's two World Cup qualifiers against Iraq and Jordan next month."
Al Habsi saw his place come under threat during the course of the season from Joel Robles, who was handed the starting berth between the posts for Wigan's memorable FA Cup final triumph over Manchester City.