The 23-year-old Willey, who played a key role last season for Northamptonshire as they won the Friends Life t20 title as well as promotion to Division One of the LV= County Championship, is struggling with a lower back injury.
Willey will now return to his country for further rehabilitation, the ECB confirmed in a statement.
The England Performance Programme squad play their first match of their tour this week when they take on Queensland IIs in a three-day game in Brisbane, starting on Wednesday.
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