He has strained medial ligaments in his knee, a similar injury to that of Latics striker Henri Camara.
Webster's agent Charles Duddy said: "Andy had a scan yesterday and it showed that he has moderately strained his ligaments.
"He will be out for six weeks. It could have been worse but it is still six weeks. But he is in the best hands now."
On the transfer front, the club are being heavily linked with a move for Crystal Palace midfielder Ben Watson.
The centre midfielder impressed for Palace during their spell in the top flight and is being tipped to join the Latics by the end of the week.
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