The song, which is a collaboration with South African band Freshlyground, was released to radio stations last week, but has not hit the right note with football fans.
"It's horrible," said fan Lindi Munonde. "I'm not standing for it. I mean what is our president doing about it?" Waka Waka - Time for Africa is inspired by Cameroonian music.
But South Africans are not convinced that the Colombian singer is the right person to represent Africa's first World Cup.
"Really, I mean, how is Shakira going to sing the African part of it?" said Johannesburg fan Nomaswazi Thomo. The 33-year-old star will sing.
The new anthem with Freshlyground before the World Cup final on July 11 at the 94000-seat Soccer City stadium near Soweto. Shakira is also one of a string of international acts performing at Fifa's Kick-off concert on June 10. The concert line-up includes US artists Alicia Keys and the Black Eyed Peas.