Buyers have been purchasing cocoa at full price from farmers since the main harvest season began in the world's No 2 cocoa producer on October 7.
But some have seen their profits hit as Cocobod, which purchases cocoa from the buyers to export, has been classifying quantities of beans as substandard, paying just 50 percent of the agreed price.
Some buyers said they were demanding Cocobod relax its grading system and were refusing to buy cocoa until the issue is resolved.
"We are not in the business to make losses, so we won't buy. The long and the short of it is we are not buying," one buyer, who asked not to be identified, said.
It was not immediately clear to what extent the row would delay or reduce cocoa deliveries from Ghana.
Produce Buying Company, by far the largest buyer in Ghana and a subsidiary of Cocobod, was continuing to buy cocoa, an official at the company said.
Another of the protesting buyers said: "Our cocoa going to the port is being categorised as substandard.
The cocoa is fantastic this year, they're just trying to pull a fast one".
Cocobod was due to meet with buyers later on Monday to discuss the dispute.