Hundreds of refugees who have been living in a church in the South African city of Johannesburg and told to vacate by December 31, are still in precarious situation without alternative accommodation, according to a church leader.

Bishop Paul Verryn, whose leadership at the Central Methodist Church ended on Wednesday, told Al Jazeera that despite the ongoing need to look after refugees, many “had wanted the refugees to leave a long time ago”.

“I don’t think everyone at the church had welcomed this project to allow refugees to live here,” he said.

“I don’t think we can ever get away from the responsibility the faith communities have towards the needs of the vulnerable, [but] they have been antagonistic towards the project.”

At last count, around 500 people were at the church on Christmas Eve, but since the evictions began on December 31, it is unclear how many are left, though some estimates suggest that up to 200 people are still at the church.

Since 2000, the Central Methodist Church in central Johannesburg became something of an institution for refugees from a host of African countries, particularly Zimbabwe, looking for a new life.

The church provided shelter, counselling, medical services, education for children and even skills development.

Verryn said helping refugees has been difficult and divisive issue, especially when so many South Africans needed help themselves.

“We have a country that is fairly unfriendly to refugees. We have a cold prejudice to them … it’s been a very difficult journey for many,” he said.

After the xenophobic riots in May 2008, that left 62 people dead, the church became even more important as a safe house for asylum seekers and refugees from across the continent.

At one point, some 2,000-3,000 people were squeezed inside the church premises, raising the ire of local government.

Some estimates suggest that since 2000, more than 30,000 refugees have passed through the doors of the church at one point or another.

Verryn said decision to quit was a personal choice. He would be engaged in skills development and anti-poverty initiatives. But he says the church “had battled over the past decade and it cost us dearly”.

“It is one of the reasons the church has come to a juncture,” he said.

The decision has raised concerns among the refugee community and activists that enough has been done to protect those vulnerable families with nowhere to go.

Ambrose, 33, a refugee from Zimbabwe and a security guard working at the church for the past eight years, said he was disappointed that the service was being dismantled without the creation of viable alternative.

“I don’t blame anyone for this. Its not a situation that you blame anyone, but the facts are the facts. Most Zimbabweans started a new life here because of this church,” he said.

“By saying people were not able to come here, they are saying that people must sort themselves out, that they wouldn’t find support anymore,” Ambrose said.

In a statement released by South African NGO, Sector 27, and signed by a legion of civil society organisations, the NGO called on government to assist in an issue that had been flagged numerous times in the past.

“If the church were to be closed – as has been threatened — the people who need its support would not miraculously evaporate, and neither would the ongoing crisis in Zimbabwe.

“Refugees would be dispersed and forced underground into places where they would be less accessible and in greater danger of health and human rights violations” Al Jazeera