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"The public protector is investigating allegations of maladministration, corruption and unconsumable use of public funds by municipalities of the Eastern Cape... ," spokeswoman Kgalalelo Masibi said.
This related to procurement of service providers for Mandela's memorial services and funeral.
Masibi could not immediately say who made the complaints.
She said the provincial government appointed the Eastern Cape Development Corporation as a provincial host and paymaster for the logistical arrangements and the funeral.
The Nelson Mandela metropolitan, OR Tambo, King Sabata Dalindyebo and Buffalo City municipalities were appointed as well, she said.
Madonsela would investigate the municipalities.
They allegedly spent nearly R65 million on service providers for Mandela's funeral without following proper procurement procedures.
Mandela died at his home in Houghton, Johannesburg, on December 5, aged 95. He was buried his homestead in Qunu on December 15.
On Friday, the Mail & Guardian reported that the Hawks were investigating how R250,000 appeared in Eastern Cape premier Phumulo Masualle's bank account around the time of Mandela's funeral.
On Wednesday, the Democratic Alliance said it had raised questions about Masualle's personal bank account in the Eastern Cape legislature, but on two occasions its questions were blocked.