Atherton, who is here as a broadcaster, had tried to take a close look at the wicket, which has generated a great degree of controversy after Mukherjee slammed Indian skipper M.S. Dhoni for asking for a square turner from day one of the Dec 5-9 game against England.
Seeing Atherton, Mukherjee went up to him and angrily gestured to him to leave the spot. "Please go!" the 83-year-old Mukherjee was heard telling the ex cricketer.
Atherton, however, left immediately without a word.
The incident happened during the net session of the Indian cricket team.
The Cricket Association of Bengal, the local staging unit, stood by Muherjee.
"How can a commentator suddenly go to the pitch? The host broadcasters are allowed to inspect the track for their pitch report only a short while before the match begins. I don't see anything wrong in Mukherjee stopping him," said CAB joint secretary Subir Ganguly.
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Meanwhile, there were evidently cold vibes between the curator and the Indian captain when Dhoni went up to the 22 yard strip accompanied by coach Duncan Fletcher.
As the duo inspected the wicket, Mukherjee remained seated outside the boundary line.
While returning, Dhoni again ignored the curator, who was seen chatting with Indian star player Gautam Gambhir on the boundary line.