Fifteen women were raped in a church by a mob of Muslims in eastern Uganda as a punishment against a pastor who was allegedly converting Muslims to Christianity.

The pastor is still missing along with eight other Christians two weeks after the attack in which the congregation were locked inside the church and several Christians were beaten, sources told Morning Star News.

Around 90 Muslims broke into the evening prayer meeting where some 80 Christians had gathered at the Katira Church of Uganda, in the Katira village, Budaka District at about 8:30pm on January 15 and beat the Christians with clubs and sticks, the report said.

A member of the congregation who escaped before the doors were locked heard one of the attackers shout, "Away with the pastor who is converting our Muslims to Christianity."

The pastor, Moses Mutasa had been outside talking to some visitors to the church when several others arrived shouting, "Away with the pastor," and he fled, according to Rev Musa Mukenye, who oversees several churches in the district's Iki-iki County.

"We do not know what has happened to our pastor, Moses Mutasa," Mukenye told a meeting of local officials, police and other security officers. "He might have been killed or has been kept hostage."

Around 50 men and 30 women had attended the prayer meeting and the assailants locked about half of the total inside the building, beat the men and tied them up before raping the women, Morning Star News reported.

"Women's clothing was found inside and outside the church building," a church elder said.

The abused women received treatment at a clinic in Katira.

Police reportedly arrived about two hours after the assault began.

Several church members were also injured as they were trampled in the rush to get out of the building, and a considerable amount of church property was damaged.

Prior to the attack, Muslims had thrown stones on the roof of the church building to disrupt services at the church, which attract 500 people.

On the morning after the attack, a group of Christians were planning to destroy the local village mosque but Pastor Mukenye pleaded for them to adopt an attitude of forgiveness, and they refrained, he said.

Pastor Mukenye said that Christians should leave justice to authorities. "This act is evil, and police should not relent until the attackers are arrested and charged in a court of law," he told Morning Star News.

The attack is the latest in a series of persecution incidents against Christians in eastern Uganda.

Around 85 per cent of the population of Uganda is Christian and 11 per cent Muslim, with some eastern areas having large Muslim populations.