"It's been repaired in two areas," said Hayden. "A hole on one end has been mudded together to stop the cracks and at the other end there was a huge hole last night and it's been repaired. It's very embarrassing. In Test cricket the rules are very plain. You can't touch any of the playing surface."
Hayden said the Australians brought the repairs to the attention of the umpires at the start of play. Match referee Chris Broad ordered that the repair work be undone, which happened during the first drinks break.
Enver Mall, chief executive of the KwaZulu-Natal Cricket Association, disagreed with Hayden's description.
He said soil was put into a hole, "about one centimetre by one centimetre" on a bowling follow-through area and taken out by groundsman Wilson Ngobese during the break.
"The Australians complained to the umpires and they were happy for play to carry on until the drinks break when the soil was taken out. The match referee hasn't made any complaint to me or the groundsman," said Mall.
South African coach Mickey Arthur said his team had been unaware of the issue until Broad entered their dressing room about 40 minutes after play had started and told them about the instruction to restore the pitch to its previous condition.
Arthur said the damage had been caused some distance outside a left-hander's off stump. "It was on about the second step of Andre Nel's follow through."
With the Australians pressing for a win, the possibility of leg-spinner Shane Warne being able to exploit any assistance from the pitch was a factor in their complaint.
"It may have come into play, it may not have," said Hayden. "But it's the principle. You never compromise those rules. It's very disappointing."
When bad light ended play, South Africa were 29 for no wicket in their second innings after being set to make 410 to win.