Mashaba said he met with provincial police commissioner Deliwe de Lange and the city's MMC for public safety Michael Sun on Tuesday night "to form a joint operation and restore order in the communities".
"According to reports, the protesters within the community are calling for new housing projects, enhanced service delivery and economic development," Mashaba said in a statement on Wednesday.
"Tragically, the legitimate concerns of communities have been hijacked by criminal elements who would seek to use the protests for their own needs. A number of shops have been looted and businesses negatively affected which further impacts on economic opportunities within these communities."
Protests that started in Eldorado Park on Monday spread to other townships such as Kliptown, Orange Farm and Ennerdale in south of Johannesburg.
Residents barricaded roads with rocks and burning tyres, vowing to keep protesting until their demands for services and housing were met.
Shops were looted and damaged mostly at night. Mashaba said with a housing backlog of at least 300 000 there was "no quick fix" to the city's housing problems.
"As the city's administration, we the frustrations of the communities following years of mismanagement and neglect. We hear their plea for dignified housing and economic opportunities. I will be contacting Gauteng Premier David Makhura to formulate means by which local and provincial government can work together to address the needs of Eldorado Park community and others."
A meeting with community leaders was being planned to create a platform for engagement with the aggrieved residents, he added.