Western Cape Premier Helen Zille walked out of a meeting on Cape Town's toilet wars on Thursday after what she said was another threat by the African National Congress Youth League to make the city ungovernable.

The meeting was convened by Cooperative Governance Minister Sicelo Shiceka in a bid to resolve a dispute over provision of toilets in the Makhaza area of Khayelitsha.

It began in a community hall in Khayelitsha soon after 2pm, but Zille and City Mayor Dan Plato emerged only 15 minutes later.

Zille told waiting journalists that youth league member Andile Lili had, in the meeting, repeated a league threat to make the Democratic Alliance-controlled city ungovernable. She and Plato were not prepared to give the league legitimacy by staying on in the meeting.

"We are not going to talk with people who threaten to make the city ungovernable and break down structures," she said.

She and Plato then left.

Lili later denied her accusation.

"That is false... she never wanted to sit with us," he told reporters.

Earlier Shiceka, Zille and Plato had addressed several hundreds residents at the site of the toilet dispute.