The supermarket confirmed it does sell some imported lamb chops, cutlets and legs under the Duchy brand when supplies from British farms are not in season.
However, leading sheep farmer and breeder Gethin Havard claims the brand and supermarket are letting down farmers.
He plans to contact Prince Charles with his complaints and to appeal for his help.
Mr Havard, aged 59, from Brecon in Wales, said: "He is so pro-British farming that this seems to cut across everything he believes in.
"I've been lambing for the past eight weeks battling the elements then I go into my local Waitrose to find New Zealand lamb for sale under the Duchy Organic label."
He claimed the New Zealand lamb was inferior to Welsh lamb and was "over-fat and over-priced".
He said: "I'm very disappointed. The industry is on its knees and we are not going to get up from there unless we have some degree of loyalty from retailers.
"Instead we are getting squeezed on prices and if we can't get more loyalty from supermarkets the countryside is going to go into decline and the farming industry will disappear."
The NFU Wales president, Stephen James, said: "As the Welsh lambing season reaches its peak farmers want a commitment from UK retailers that Welsh lamb is given pride of place on supermarket shelves.
"And I would like to remind customers to check logos and labels on their purchases, both online and in store, to ensure they don't get caught out."
The Waitrose Duchy Organic brand is a partnership between Waitrose and the Duchy Originals company, which was set up by the Prince of Wales in 1990.
In fact, Waitrose sells a wide range of imported produce alongside British crops under the Duchy name.
A percentage of the value of all sales goes to the Prince of Wales Charitable Foundation, which supports struggling communities and helps young people build careers and businesses.
A Duchy of Cornwall spokesman said: "This is a matter for Waitrose - they lease the Duchy Organic brand from us and we wouldn't want to comment."
Waitrose said it operates a "best in season" policy for all its lamb, conventional and organic, to ensure customers could buy high quality lamb all year round.
A spokesman said: "During the British season, we only sell UK- farmed lamb, predominantly from Wales and the West Country.
"Outside the UK season, conventional UK lamb is always available on our service counters from a small number of our farmers who specialise in all-year-round production."
Waitrose is running a trial with some of its UK Duchy organic lamb farmers to establish the potential to extend the season of this lamb.
The spokesman said: "Overall we aim to get as many of our organic products from the UK as we possibly can.
"But in some cases, where it's simply not possible to source our total requirement for the quantity and quality we need to supply our 300-plus shops, as is the case with organic lamb out of British season, we go abroad for a proportion of what we need rather than not offer an organic choice to our customers."
