The defacement was discovered on Friday morning by workers at the building, said the council – the building had been defaced with the old apartheid flag colours of blue, orange and white.
"Those behind these acts of vandalism are people with a political agenda.
"There are people who are mobilising for a rent boycott in protest against the name changes," said the council.
The council condemned "racist graffiti" found across the city as "completely unacceptable.
They contained insults, political defiance, and attacks on black people, their leaders and government.
The council said they had lodged a complaint with the police and would be studying their CCTV cameras for more information about who was behind these acts.
The city’s new street names were being removed and dumped in the Vaal River.
Others had been defaced with black paint, said the council.
"One of the Nelson Mandela Drive street name-plates was painted with black paint to read "Dela rylaan".
"We are now convinced that those engaged in these acts of political vandalism are people with a clear political agenda," said the council.