Shami was included in his country's initial squad for the hastily-arranged contests against Sri Lanka, which are a consequence of West Indies pulling out of their tour of India.
However, the Board of Control for Cricket in India (BCCI) confirmed via Twitter on Monday that the seamer had been withdrawn, with Dhawal Kulkarni taking his place.
A tweet from the BCCI's official account read: "News Alert: Dhawal Kulkarni replaces injured Mohd Shami in the ODI squad for the first three matches against Sri Lanka."
It is not yet clear why Shami has been declared unavailable, but his absence provides Kulkarni with the opportunity to challenge for a second ODI cap.
The 25-year-old medium-pacer made his debut against England at Edgbaston in September, failing to claim a wicket in a match that saw Shami return figures of 3-28.
India begin their five-match series against Sri Lanka on Sunday in Cuttack.