"None of the rock lobster was proven to be undersized and the allegations to this effect were factually incorrect," said Jean Dennis, spokesperson for Fruit & Veg City, reports News24.
The Food Lover's Market is part of the Fruit & Veg City Group.
"For this reason, the case was withdrawn before court as there was no case," she said.
The department of agriculture, forestry and fisheries claimed that fishery officials confiscated 50kg of undersized west coast rock lobster during a raid on Friday.
At the time, departmental spokesperson Steve Galane said some of the rock lobster at the shop were found to be under the legal size of 7.5cm.
They were being sold for R50 each.
The department laid a criminal charge against the shop on Friday afternoon.
"The fact is that only 5kg were removed from the premises and all rock lobster were obtained from legitimate authorised suppliers and could be traced back to their source," said Ms Dennis.
Galane said the department would follow up on the reasons for the court's dismissal of the case.