Zimbabwean refugees should not be allowed to stay in Johannesburg's Central Methodist Church, Gauteng local government MEC Qedani Dorothy Mahlangu said on Friday.

"I think [Methodist Bishop Paul Verryn] is exposing them to more danger. We are not condoning what he is doing. We condemn it," she said.

Many Zimbabwean refugees arriving in Johannesburg congregate around the church which has been a haven for them for the past two years.

According to Verryn, the church is at full capacity and as many as 2000 more Zimbabweans are living on the streets in the vicinity.

Mahlangu said the church was not a suitable place for large numbers of refugees.

"Any church, any community hall is not meant to be inhabited by people," she said.

But despite criticising Verryn, Mahlangu promised continued cooperation with him.

"The City of Johannesburg will continue to partner with the Central Methodist Church," she said.

Johannesburg mayoral committee member for development planning and urban management, Ruby Mathang, said the process had begun.

"We've been approached by the church. They want to get a building. We're currently processing the issues of them leasing a building."

Mahlangu said government was negotiating with NGOs to provide accommodation for the thousands of Zimbabwean refugees living in the church and on the streets around the church.

She declined to name them as she said negotiations were still ongoing.

The NGO's would be better able to provide accommodation for the refugees.

She also held out the possibility that private individuals, with appropriate facilities, could house some of the refugees.

Mathang and Mahlangu said plans for the refugees would be finalised sometime next week. Mahlangu would not say how refugees who refused to be removed from the church would be dealt with.

"We'll cross that bridge when we get there," she said.

Verryn could not be immediately reached for comment.

Earlier in the week, he said he was "absolutely" concerned about the health situation in the church.

It was for this reason that Medicins Sans Frontieres (MSF) has been operating a clinic in the church.

Last Sunday, one of the refugees in the church was diagnosed with meningitis.

He has since recovered and those closest to him were treated with prophylactics.

MSF Nurse Bianca Tolboom said that since November, there had also been four cases of cholera in the church.

On Thursday, Mahlangu's department said the UN High Commission for Refugees (UNHCR) had created a refugee crisis in Johannesburg.

Since February, the UNHCR has been providing transport for thousands of Zimbabwean refugees at the Musina showgrounds to come to Johannesburg – without first informing local authorities.

Mahlangu and UNHCR regional representative for Southern Africa Sanda Kimbimbi said that practice would be slowed, if not stopped altogether.

Zimbabwean refugees would be required to prove they had a place of residence or a job waiting for them in Johannesburg before they would be provided with transport.

Kimbimbi said many refugees came to Johannesburg in search of employment. He said refugees would now be advised that this would not necessarily be the best option.