The dispute between the local parish priest and the council is the latest setback for worshippers at the Mar Grigis al-Sawma Church in Neda. The village is located in the Sohag province in Upper Egypt, which covers a region made up of strips of land on both sides of the Nile. The council had originally accepted an engineering plan which included a bell tower with a crucifix on top and granted a building permit.
But the authority has since backtracked on its decision and said the structure will have to be removed from the drawings.
The priest has appealed to President Abdel Fattah el-Sisi to intervene and resolve the case, reports persecution.org.
The Court of Akhmim heard the case last weekend but the outcome is not yet known.
Christian worshippers in the North Africa nation have faced threats from Islamic extremists in recent years.
But this week Coptic Catholic Bishop William of Assiut said things are improving.
The church leader told Catholic charity Aid to the Church in Need: “We thank God that the situation is getting better.
“The president has goodwill towards the Christians.
But he said the ties between Muslims and Christians were strong, despite reports of tensions.
“They would like to establish an Islamic State but in Egypt it will never materialise,” he added.
“Egyptians are close – Christians and Muslims are too united for the extremists to cause problems.”
Ninety percent of Egyptian citizens are Muslim, predominantly Sunni.
Shia Muslims constitute less than one percent of the figures.
Ten percent of the overall population are Christian, the majority whom belong to the Coptic Orthodox church.
The Christian community also includes Catholics, Armenian Apostolics, evangelical Protestants and Baptists.