The department said that a meeting was held with representatives of the communities and the parties involved agreed to report back in the next 10 days.
"The community requested that the Minister intervenes and assist in finding a lasting solution for their problems."
Some of the problems highlighted included backyard dwellers, the slow pace of upgrading informal settlements, housing allocation for people outside the area, and housing for people who who have been on the waiting list for a long time.
The department said that an urgent meeting would be held on Thursday with Cooperative Governance and Traditional Affairs Minister Des van Rooyen, MEC for Human Settlements Paul Mashatile and the executive mayors of the City of Johannesburg and the City of Tshwane.
"Officials from all the affected departments and metros have been instructed to craft a long lasting response to the housing challenges in these areas. These will be presented to the ministers so that they are converted into programmes of government and are budgeted for," it said.
On Sunday, Sisulu is expected to lead a government delegation to meet representatives of the affected communities.
"Minister Sisulu has reiterated that government is serious about resolving the issues raised by the communities. She called for calm until a common ground is found."
Residents of Ennerdale, Eldorado Park and Fine Town, all in the south of Johannesburg, embarked on service delivery protest this week.
A number of shops being looted and one person arrested during service delivery protests in Ennerdale on Tuesday.
Protest action began on Monday in Eldorado Park and Freedom Park, before Ennerdale residents joined on Tuesday.
Tyres were burnt in the streets and entrances to the areas were blocked.
Both Eldorado Park and Ennerdale residents are allegedly protesting because of the lack of service delivery in their areas.