The announcement comes a matter of months after Francis warned priests of Nigeria's southern Ahiara diocese that they would lose their jobs if they did not obey him and accept Peter Okpaleke as their bishop.
It was not clear how many of them obeyed within the 30-day deadline given by Francis to accept Bishop Okpaleke last June.
But on Monday, the Vatican announced that Bishop Okpaleke is resigning and that Francis has named Monsignor Lucius Iwejuru Ugorji as Ahiara's temporary administrator.
Pope Benedict XVI had appointed Bishop Okpaleke to Ahiara in 2012, but the local clergy rejected him.
Ahiara is a very Catholic diocese of the Mbaise region, and its faithful objected to the appointment of an outsider from the Anambra region being imposed on them. The Mbaise had wanted one of their own and blocked access to the cathedral when Bishop Okpaleke was to be formally installed.
Instead, he was installed outside the diocese six months after he was appointed.
The case was a test of papal authority, and has echoes with another divisive appointment in the news concerning Chilean Bishop Juan Barros.
Bishop Barros has been rejected by many faithful and priests in southern Osorno, Chile, ever since Francis appointed him in 2015. They cite accusations by sexual abuse victims that Barros witnessed and ignored their abuse at the hands of Chile's most notorious paedophile priest.
During his installation Mass in 2015, protesters stormed the church, carrying signs saying they did not want Barros as their bishop.
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