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Although Flintoff played in all five of England's matches in the ICC World Twenty20 he was clearly in discomfort and was almost hobbling in the last game against India.
"Following the recent NatWest series in England Andrew experienced a reaction in his left ankle but subsequent scans determined no new injury had been sustained," an ECB spokesman said. "After consultations with specialists it was felt that the ICC World Twenty20 would provide a safe platform to assess how Andrew's ankle would respond to bowling in match conditions, without the risk of further damage to the ankle.
"Andrew has experienced some discomfort as the World Twenty20 tournament has progressed, but has been determined to provide a contribution to the team's performance. At no time was further damage to the ankle sustained, but unfortunately it was clear that his ability to increase the intensity of his rehab and participation could not be progressed.
"Accordingly, after ongoing review and discussion with specialists, it is felt that the appropriate course of action is to allow time for the ankle joint to settle and recover before the process of further strengthening and assessment of the ankle is intensified."
The spokesman added that Flintoff had not been ruled out of the Test series in Sri Lanka which starts in late November.