Reverend Alan Storey, who was a part of the delegation, said he was not attacked.
"We are asking people to remain calm, peaceful and patient. We are doing our best to resolve everything," he said.
In Gauteng, police were removing refugees camped at the UNHCR offices in Pretoria on Friday.
On Wednesday the high court in Pretoria ordered foreign nationals to vacate the area.
A group of refugees stormed the UNHCR offices in Brooklyn, Pretoria, on Thursday.
Archbishop Thabo Makgoba attacked in refugee chaos at church in Cape Town
Irate foreign nationals who took refuge at the Central Methodist Mission Church in Cape Town, fearing xenophobic attacks, attacked faith leaders on Friday.
Chaos erupted at the church in the morning while faith leaders were announcing plans for relocation, repatriation and reintegration of the foreigners.
More than 200 refugees have been living in the church for weeks after police moved them from a makeshift camp outside the premises of the UN High Commissioner for Refugees' (UNHCR) in the CBD.
Anglican Archbishop Thabo Makgoba, who was caught up in the fracas, confirmed the incident, but pleaded for sympathy and understanding.
“One doesn’t expect violence to break out at a sanctuary, but when I put on my psychology hat, this is what we call termination anxiety. We are dealing with a human issue here, a desperate situation," he told SowetanLIVE sister publication TimesLIVE.
“We were telling them something they didn’t want to hear, so the reaction is somewhat justifiable,” said Makgoba.
“They started attacking one reverend who was on the stage and some of us caught the fire too. At least my wife likes the tiny injury on my forehead. She calls it a dimple.
"I was in the right place at the wrong time. We are worried about their health and safety at the church. It would have been better if we could provide a better solution," he said.
The South African Human Rights Commission (SAHRC) was briefing the refugees on conditions under which individuals can be repatriated.
Commissioner Chris Nissen said some people in the group was not willing to understand. He was also attacked and sustained head, finger and knee injuries.
"Tempers are high, but we urge them to understand this is not a group activity. Individuals must apply and we look at it case by case. They kept telling us they no longer want to be in South Africa, but it depends on what we can do," Nissen said.
Reverend Alan Storey, who was a part of the delegation, said he was not attacked.
"We are asking people to remain calm, peaceful and patient. We are doing our best to resolve everything," he said.
In Gauteng, police were removing refugees camped at the UNHCR offices in Pretoria on Friday.
On Wednesday the high court in Pretoria ordered foreign nationals to vacate the area.
A group of refugees stormed the UNHCR offices in Brooklyn, Pretoria, on Thursday.