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Ifill had the surgery to clean out his right ankle, and physiotherapist Wayne Roberts said it would be four to six weeks before he is back in action.
Head coach Ricki Herbert said it was disappointing to lose such an influential player over what is a busy period, but it was in the best interest of the striker to have the operation immediately.
"The injury has obviously been affecting Paul's form and, rather than wait until the end of the season, I felt it best to get it done now," Herbert said. "It is in his best interest, and ours, to have him back to his best for the rest of the season."
Ifill, who has been the club's best player since his arrival in 2009, has been out of sorts this season and often been substituted early in games. He was also the subject of racist abuse in Wellington's 3-1 defeat to the Reds in Adelaide on Sunday, an incident that is being investigated across the Tasman.
The Phoenix, who are seventh on the A-league ladder, take on Central Coast in Wellington on Saturday. Jeremy Brockie, who missed the last game with a hamstring injury, is the obvious replacement for Ifill in the starting side.