The Prince of Wales has been dropped by Sainsbury's as a supplier because it says his organic vegetables do not meet the right standards.
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Sainsbury's cited "quality issues" with the carrots from Highgrove.
A Clarence House spokeswoman said there were "difficulties relating to packing, distribution and storage".
The store has also stopped accepting carrots from Patrick Holden, the head of the Soil Association, who blamed the centralisation of supply.
Mr Holden told BBC Radio Five Live his carrots were being sent by truck from his farm in Wales to a packing plant in Peterborough.
Once wrapped, they were then delivered back to eight Sainsbury's stores near his farm via a depot in Bristol.
Mr Holden, director of the organic food and farming charity, said he was de-listed because of "quality issues", which were "at least in part caused by transport".
"The truth is if you buy your carrots in Sainsbury's, they will only come from this one pack house in Peterborough," he said.
"I haven't got anything in for Sainsbury's. My issue is that all supermarkets have adopted this policy of centralisation of supply."
He said he and Prince Charles were "casualties" of the system, which impacted on thousands of small farms and caused products to have larger carbon footprints.
Mr Holden and the Prince's farm in Highgrove, Gloucestershire, were sacked as suppliers of carrots at the end of January.
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Sainsbury's said there were "significant" quality issues with the carrots from Highgrove, branded Duchy Carrots, because they had been stored for three to four months before being taken to the packing plant.
A spokeswoman said: "Our priority has to be fresh, quality produce or customers will not buy it.
"We have already gone to great lengths to help these farmers and will continue to work with them to find a solution."
A Clarence House spokeswoman said the "short trial" to provide a small number of carrots ended with Sainsbury's decision not to continue stocking the vegetables.
"There were difficulties relating to packing, distribution and storage," she added.