Just over 94 percent of polling stations countrywide were reported open shortly before 9am on Wednesday, the Independent Electoral Commission said.
"But this does not necessarily mean that the remaining six percent are not open," IEC official Mosotho Moepya said at the results operations centre in Pretoria.
He explained that the SMS network used by polling station presiding officers to alert the IEC of their status sometimes got clogged, resulting in delays in confirming that some stations were open.
"I estimate the real figure to be closer to 98 percent." All voting stations were supposed to have opened at 7am.
Moepya said torrential rains in parts of Limpopo may have caused some delays in opening.
But Limpopo was one of six provinces which reported that 100 percent of their stations were open by 9am. The others were the Eastern Cape, Gauteng, Mpumalanga, Northern Cape and Western Cape.
The Free State stood at 93.2 percent and the North West at 86,7 percent, while KwaZulu-Natal had the lowest rate at 78.3 percent.
"In the case of KwaZulu-Natal, I know the problem is one of reporting," Moepya said. "I am not too worried." - Sapa