The government is considering taking court action against the Central Methodist Church, in Johannesburg, to remove children from the premises, the Gauteng department of health said.

"Over the past fortnight we had several meetings with the Church," said spokesman Simon Zwane.

"[We agreed] the children would be there on the 7th [Monday]. There was no-one from the Church to assist with the process. The principal wasn't there and there were children who ran away."

Zwane said the department's visit that day was in agreement with the church and Bishop Paul Verryn as part of a "process of engagement".

However, social workers were left feeling "frustrated and undermined".

A court order would allow government officials to enter Church premises when they wished to remove children and place them in shelters.

"If we have a [court] order we can come anytime," said Zwane.

He said that the government was working with non-governmental organisations to place the children. So far, 54 children from the Church have been placed in shelters.

On Tuesday, over 30 civil society organisations including the Aids Law Project, the South African Council of Churches and the Congress of SA Trade Unions issued a statement in support of Verryn and the use of Central Methodist Church as a shelter for migrants.

They said that while the Church was not an ideal place, it was better than many of the alternatives.

Some of the people who had been moved from the church to shelters had since returned, they said.

The Church was expected to comment later.