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"We don't enjoy cutting off [electricity to] people, but the municipality has a legal responsibility and obligation to collect all the money due to the municipality," he said in Parktown.
He said the City would not "wrongfully" cut power.
The widespread billing problems in the City of Johannesburg, the country's economic hub, has angered many residents.
Masondo said "significant progress" had been made in dealing with the situation. He earlier drew widespread criticism for saying that the problem did not constitute a "crisis".
He could not provide a timeline of when the billing issues would be resolved.
"In one year's time, in two years' time, many of the problems... will be problems of the past," he said.
Masondo was speaking at a media briefing on the sidelines of a meeting called by the ANC in Gauteng with all mayors and managers in ANC-led municipalities.
Grave concern
The ANC expressed "grave concern" over the billing problems.
"The billing problems in Johannesburg had reached crisis point at a certain point. We have reached a different level now," said ANC Gauteng secretary David Makhura.
Measures were put in place to address the problems.
Masondo said "more and more" municipal staff now had a better understanding of how the system worked.
Nominations
The response of mayors to the billing hassles and to the recent floods would influence their nomination as ANC candidates in the upcoming local elections, said Makhura.
"That is an important issue to look at when we will be making decisions on candidates for mayors," he said.
"We are being sensitive to the fact that people are being affected... We are saying to mayors, don't blame residents... Help them, talk to those affected," he said.
"That's a very important consideration."
Makhura told mayors that every complaint their municipalities received was "one too many".
"As the ANC, we will never be satisfied... We want a completely reliable billing system. We will always be on the side of those affected," he said.
System
He said the ANC did not believe the problem was with the system.
"We know the problems are not with the system... metros have invested in the modernisation of the system.
"In Johannesburg there was a great deal of neglect by those on the frontline tasked with providing leadership to municipal officials," he said.
He said the ANC was satisfied with Masondo, as he had done a lot to improve under-developed areas such as Soweto.
The ANC runs 13 of the 15 municipalities in Gauteng.
The ANC called the meeting with mayors and municipal managers to discuss the billing problems, flood damage and the managing of finances.
