The row began when Clergymen in the diocese of Ahiara in Imo State, refused to accept the appointment of a bishop made in 2012 on ethnic grounds.
During talks in Rome with a Catholic delegation from Nigeria, the pope demanded that priests and church members in the diocese of Ahiara write to him personally to "ask his forgiveness".
The Holy See stated the pontiff said: "In the letter, one must clearly manifest total obedience to the pope, and whoever writes must be willing to accept the bishop whom the pope sends and has appointed."
Bishop Peter Okpaleke - who was appointed by his predecessor, Benedict XVI is from Abia State - Imo's neighbouring state.
Pope Francis claimed the "people of God are scandalised" by what happened and gave the clergy until 9th July to obey his directives.
Ever since Bishop Okpaleke was appointed, the BBC reports the president of the Catholic Bishops Conference of Nigeria, Archbishop Ignatius Kaigama, has been part of a group trying to persuade the clergy in Ahiara, to accept the appointment.
Explaining the priests' grievances he said the local clergy and bishop were from different clans of the Igbo ethnic group which led them to question why someone from outside the diocese was appointed.
In 2012, the clergy held protests and coordinated petitions asking for a bishop to be chosen from the area.
Archbishop Kaigama attended the meeting in Rome and said that the pope was very sad about what was happening and he could see "the pain in his eyes".
He added: "He was upset that his children were going in a different direction."
It is not clear if the clergy has responded to the ultimatum.
