The board said the move will cost some of its members thousands of dollars.
Currently, most farmers sell potatoes in five, 10, 15, 20 and 50 pound bags. But when the rules change, the board said they'll have to provide whatever the grocery stores ask for.
That means having more packaging on hand in more sizes that farmers might not even use.
Gary Linkletter, a farmer who is on the P.E.I. Potato Board, said he's worried $300,000 worth of potato packaging in his inventory will go to waste.
"Under these new changes, any size, like you can have a seven pound, you can have a two kilogram, a four kilogram, you can have an eight pound, a four pound and so it becomes the cat's meow," said Linkletter.
He questions why the government is making the changes. He said no one in the industry was calling for them and said customers may be confused by the changes.
"They'll have to start looking really carefully at what they're buying," said Linkletter.
"Right now, if they grab a smaller bag, they know it's a five pounder. If it's a bigger bag, they know it's a 10 pounder. Now, they'll have to start looking, 'Am I paying that money for a 7 pounder? Am I paying that money for an eight pounder? What am I getting for my money?'"
The government said the changes are in the customer's best interest.
Agriculture minister Gerry Ritz told CBC in a statement, "The Canadian Food Inspection Agency's first priority is food safety, which is why they are transitioning out of non-food safety regulations such as this."
Ritz said the changes give consumers more options at the grocery store. Linkletter said those choices may end up costing consumers.
"Ultimately, we have to get our money back from the marketplace. So if we end up putting another $150,000 to $200,000 of inventory on our floor, at some point an time we've got to have that covered up, and there's only one place it comes from and that's the consumer," Linkletter said.
A spokesperson from the CFIA said the agency has taken stakeholders' input into consideration. It said the changes will be brought in gradually and it said it will work with industry to allow enough time for transition.