The supermarket said the move was in response to concerns within the medical community that consumers were not including enough sources of omega 3 in their diets.
The birds, produced by Moy Park on family farms in Northern Ireland, have been fed on aquatic plants including kelp and seaweed - naturally rich in the polyunsaturated fatty acids.
The taste and appearance of the chicken is the same as birds reared on a conventional diet.
As a key part of a balanced diet, Omega 3s help to maintain normal heart, brain and vision function.
Research undertaken in 2013 showed people with the highest levels of omega 3 had a 40 per cent reduction in cardiovascular related deaths compared to people with the lowest levels.
Optimum health benefits are obtained from a daily intake of 250mg of omega 3 fatty acids as part of a healthy balanced diet and lifestyle.
Despite leading authorities recommending regular consumption of foods containing omega 3, research suggested only 23 per cent of the UK’s adult population consumed the recommended intake, generally classified as at least one portion of oily fish per week.
Statistics showed intake levels were particularly low in children and young people.
Chicken is the retailer’s top selling protein.
Heather Jenkins, Waitrose’s agricultural director, said: “Our research is showing that this nutritional breakthrough has the potential to have a significant impact on health.
“What’s exciting is that it’s improving the nutritional content of something which customers already consume frequently as part of their diets.”
Professor Chris Elliott, pro vice chancellor, Faculty of Medicine, Health and Life Sciences, at Queen’s University Belfast, added: “It’s costing £10 billion a year to deal with problems of heart disease in the UK. Having a source of omega 3 in our diet has the potential for healthier hearts.”
Ten different new products, including whole chickens, breast fillets and thigh meat will go on sale from June 15, priced from £3.59 per kilo.
Omega 3 levels vary depending on the specific cut of chicken.
However the following portions would provide a full daily allowance of omega 3s: