They had been charged with murder and conspiracy to murder, as South Africa does not have a specific charge of cannibalism.
Prosecutors told a court in the farming town of Estcourt that the charges against the three had been provisionally withdrawn, and they may or may not be re-instated at a later stage, the Estcourt and Midlands News site reports.
AFP news agency gives a different account, saying the three had been acquitted because of a lack of evidence.
Four other men charged with them remained in police custody.
Police fired rubber bullets and stun grenades to disperse crowds of people who hurled insults at the accused as they appeared in court, AFP news agency reports.
The men sat in the dock, hiding their faces with their hands and hooded tops, it adds.
The seven were arrested after police said one of them walked into a police station in August with a leg and a hand, and said he was tired of eating human flesh.