Following the closure of a number of churches in recent weeks, Coptic Christians in the south of Egypt have renewed calls on local authorities for an end to discrimination.

Two churches in two separate villages in the southern province of Minya have been shut down by the authorities, a statement by the Minya diocese said.

It said worshippers were harassed at both churches and pelted with rocks at one of them.

'We have kept quiet for two weeks after the closure of one of the churches, but due to our silence the situation has worsened ... it is as if prayer is a crime the Copts must be punished for,' said the statement, which was released on Saturday.

A third church was closed following rumors of a pending attack, but the diocese said no attack has taken place since and the church remains closed.

The Minya security directorate spokesman declined to comment. The governor's office did not immediately respond to a request for comment.

Coptic Christians, who make up 10 per cent of Egypt's population of nearly 95 million, say they have been persecuted for years. Many feel the state does not take their plight seriously enough.

Nonetheless, the Copts are vocal supporters of President Abdel Fattah al-Sisi, who has vowed to crush Islamist extremism and protect Christians. He declared a three-month state of emergency in the aftermath of two church bombings in April which has since been renewed.

Though Islamic State has long waged a low-level war against soldiers and police in Egypt's Sinai peninsula, it has stepped up its assault on Christian civilians in the mainland.

In an attack claimed by the group in May, gunmen ambushed a group of Coptic Christians traveling to a monastery in Minya, killing 29 and wounding 24.

Additional reporting by Reuters.