Graeme Smith and Russell Tiffin exchange views after Andre Nel had been warned for running down the pitch on the second day © Getty Images

The third day of the first Test between New Zealand and South Africa got off to a controversial start when the groundsman was ordered to reverse an overnight repair to the pitch.

Clive Lloyd, the ICC match referee, told Karl Johnson that an area he had plugged with cement on a length outside the right-hander's leg stump was not acceptable, and instructed him to remove the filling.

The repair was brought to Lloyd's attention by the South African management, and he agreed that the repairs were excessive. Johnson said before the match that preparing the pitch at Hamilton had been difficult, because of heavy rain in the build-up to the Test.

In a statement, Lloyd said: "There was some miscommunication between the ICC playing-control team and the turf manager at the close of play yesterday. As a result the turf manager believed he had been instructed to secure several loose pieces of turf back in place.

"The condition of the pitch should not be artificially altered during the match. Before the start of play today I instructed that the pitch be returned to the condition it was in at the close of play last night."

On the second day, Andre Nel was officially warned by Russell Tiffin for running on the pitch after bowling two balls. An exchange then followed between Tiffin and Graeme Smith.

Eric Simons, the South African coach, outlined his side's objection to the pitch repairs before the third day. He also mentioned that changes that had been made to the sightscreens before the third day began.

Simons said that the South Africans had wanted to have a look at the pitch after play on the second day because it had broken up in several areas. "We came in this morning and some work had been done, which is obviously not correct, and the match referee corrected that later in the morning. It's the first time that has happened to us and it was rather strange."

Simons said that after their arrival at the ground they had noticed that work had been done and they brought it to the attention of the referee. The South Africans had taken photos the night before, because there had been some indication that work would be done on the pitch.

"We went and had a look at the wicket, a group of us, we turned to leave and overheard a conversation which made us nervous. We took some photographs," explained Simons. "The pitch was repaired this morning, which was disappointing. I'm not sure what happened."