A MyCiTi bus was stoned in Khayelitsha amid an ongoing "wildcat" strike by drivers who are demanding insourcing and better working conditions.
Transport mayoral committee member Brett Herron said no injuries were reported to him.
He said buses would now depart from Kuyasa station with protection from law enforcement.
"[The] N2 express service has operated throughout the week without being impacted by the strike. It seems their (MyCiTi) staff who did not go on strike are targeted for intimidation now," he said.
Herron said a police case was opened.
"Those who are intimidating or attempting to disrupt services must be arrested."
The City's law enforcement director Robbie Roberts confirmed a report of petrol bombs thrown at a bus while it was at the MyCiTi bus station in Kuyasa on Monday.
It was not immediately clear whether it was the same incident that Herron spoke of.
The illegal strike started last Monday, disrupting services on several routes around the city.
As of Tuesday morning, the following routes are not operational: A01, D03, T01, T02, T03, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 114, 213, 215, 216, 230, 231, 235, 251, 260, 261 and 262.
The City obtained an urgent court interdict last week.
The Western Cape High Court interdict sought to prevent strikers from intimidating, harassing or assaulting MyCiTi passengers and staff; damaging MyCiTi stations, depots or buses; and gathering at, or coming closer than 100m to MyCiTi stations, depots or buses.
MyCiTi workers have vowed to stretch their strike into its second week despite the interdict.
Striking drivers, supported by the EFF, have consistently gathered outside the Civic Centre to meet with Herron.
Herron, who said he believed the strike was "orchestrated by the Economic Freedom Fighters for their own narrow political interests", maintained that he would not engage with the strikers through the EFF.
"Discussions about employee concerns cannot be brokered by the EFF, who have instigated this strike and have no role to play. I will not participate in an EFF political show," he said.
"I have been available all week long to address the striking workers, but on the condition that this engagement happens through their legitimate representatives, namely the unions who represent the employees in the workplace," Herron confirmed.
But the strike's leaders made it clear last week that they wanted the EFF to be included in any negotiations with the City.
One of the striking workers' leaders, Johannes Gordon, said they decided to approach the EFF because their union could only do so much for them.
'Not turning back'
"We went to the EFF for help because our union can only go as far as the bargaining council. We have had enough of the bargaining council because it benefits the employers and not us."
He said they were adamant about their demand for insourcing and were "not turning back".
"We want to work for the City straight, and not labour brokers, because every time when something happens and we ask the employer about it they tell us that 'the City decided so'," Gordon said on Monday. He added that some of the workers had received dismissal letters from the employer.
Gordon said unions had until November 2 to oppose the interdict.
He insisted their strike was a peaceful one as they had no intention to damage buses or intimidate drivers. "As much as they say we do so (intimidate drivers), we are not here to intimidate. If there is a driver being intimidated then it might be a personal thing from some individual or so," he said.
National Union of Metalworkers of South Africa (Numsa) regional general secretary Vuyo Lufele said there were no new developments regarding the demands of the workers.
He said a meeting was expected to take place on Wednesday. He added, however, that the meeting had not been organised by the union but by ANC and EFF members.
Lufele added that the union had tried for a long time to help workers with the issue of insourcing, but was limited in what it could do.
"We have limited powers as the trade union. We have a relationship with the employers who employ our members, but when our members came to us about these issues we said let's try," he said.