Cape Town mayor Dan Plato has encouraged church organisations to engage in meaningful discussions with the city so that legal alternatives to illegal structures on city-owned land can be found.

"Ultimately we hope that the various church organisations and the Western Cape Christian Ministers Forum will understand the difficult position in which we find ourselves," Plato said in an open letter to the forum.

The issue of the demolition of allegedly illegally built structures by the city's anti-land invasion unit exploded this week, with officers of the unit allegedly attacked and chased away by Khayelitsha residents and opposition politicians slamming the DA and its leader, Helen Zille, over the issue.

Religious leaders claimed the anti-invasion unit had been demolishing churches' informal structures since last year.

Plato said in his letter that "in the spirit of public engagement and in an attempt to reach mutual agreement" the city had met representatives from various church groups on several occasions since 2008, to hear their concerns and explain the city's position on the demolition of illegal structures.

While the city was empathetic to the plight of church leaders, it had to be understood that it could not make exceptions where structures were illegally built on city land, Plato said.

"This is a policy that is applied city-wide, and for example, very recently action to stop building was taken in Clifton and Rondebosch," he said.

Plato said churches had been erecting structures - many of them not temporary in nature - without permission or submission of plans, and without compliance with health and safety regulations.

He said the demand for viable city land - from schools, creches, churches, shopping malls and other facilities - exceeded supply.

Legislation regulated the dispensing of land, requiring public participation to take place whenever viable city land was made available for development.