"It was a very difficulty decision for us to take," he told reporters in Pretoria.
The department would play no part in the weekend's event.
"We have not been provided with the necessary assurances as to the state of readiness that would have made this event possible. We regret that the names of artists have been used to promote this event without their consent," he said.
Wakashe said the department had allocated R4 million to sponsor local and international artists and R3 million of this had already been paid to Morris Roda Productions.
Adviser to the minister David Dlali said the matter would be heard at 2pm in the High Court in Pretoria on Thursday.
"One of the issues is to recover the R3 million that has not been given back," he said.
Wakashe said the company had been informed of the cancellation of the contract and he had been in contact with the Makeba family.
"We have approached the family, we have been in conversation since last week and yesterday I meet with the family."
When asked how the family felt about the withdrawal of support for the tribute, which was scheduled from Saturday to Monday, he said: "It's not a question of whether we are disagreeing or not. We would all have loved to see this going through."
The department pledged to support the event after the Makeba family had already contracted Morris Roda Productions.
"We had hoped to still honour Mama Africa on the anniversary of her death on November 9 through the event initiated by her family.
"The department will continue with its legacy projects in honouring icons of our country and hope to highlight the contributions of Miriam Makeba in the near future," said Wakashe.
One of the artists involved told journalists in Johannesburg that it would go ahead.
"This thing is far beyond Morris. Artists have taken a whole year to rehearse and we will not budge. We are going ahead as planned on Saturday," said musician Mzwakhe Mbuli, a member of Vhutsila Arts, an events company working with Morris Roda Productions.
Mbuli said they did not need permission from family members to celebrate their icons, while Morris Roda refused to comment, saying it was sub judice.
The event, which was supposed to have been held at the Union Buildings, has now been moved to Church Square in Pretoria.
Makeba passed away on November 10, 2008 aged 76.
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