Ellis, who is not part of the Test squad currently in England, was injured in training and will not be joining the Black Caps one-day squad for the tournament, or their one-day series against England.
No replacement has yet been named.
Cricket New Zealand confirmed: "Canterbury all-rounder Andrew Ellis has been withdrawn from the Black Caps squad for the ICC Champions Trophy due to a broken rib.
"The 31-year-old suffered the injury while training in Christchurch in preparation for both the ICC Champions Trophy and a three match one-day international series against England."
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