The two retailers respectively scored 6.5 and 8.5 out of 29 in the survey, which graded 25 British food and household goods companies on their progress towards sourcing sustainable palm oil.
The oil can only be grown in the tropics and its increasing production has led to rainforests being cleared, impacting wildlife such as orang-utans in countries including Malaysia and Indonesia.
Nature charity WWF wants companies to buy oil that meets environmental standards, certified by the Roundtable on Sustainable Palm Oil (RSPO), which is between 10% and 20% more expensive.
It said 14 out of the 25 companies had not bought any RSPO oil: in order of lowest-scoring to highest they are Aldi, Associated British Foods, Croda International, Boots, Warburtons, Britannia Food Ingredients, Waitrose, Morrisons, Jordans Ryvita, Northern Foods, Reckitt Benckiser, Co-op, Premier Foods and Tesco.
Last year at the offices of the company and agencies Ogilvy and Lexis PR in a bid to pressure it to change the behaviour of its palm oil suppliers.
The Dove manufacturer scored highly in the survey with 24.5 points out of 29.
It was one of 11 companies that had bought RSPO oil: in order of lowest-scoring to highest they are Burton's Foods, United Biscuits, Asda, The Body Shop, Cadbury, Unilever, Young's/Findus, Marks & Spencer and Sainsbury's.
Boots, which joined the RSPO in 2006, claims it uses palm oil derivative products of which sustainable versions were not yet commercially available.
In a statement it said: "As a pharmacy-led health & beauty retailer, our use of palm oil is minimal compared to other industries. Unlike the food industry, the majority of our exposure to palm oil usage is via derivatives from a wide variety of sources.
"At the present time, sustainable sources of palm derivatives are not commercially available, hence our score in this report which we do not feel reflects our commitment to this subject.
"We continue to work with our suppliers to identify if these can be obtained from sustainable sources."
Waitrose, which became a member of the RSPO in 2006, said: "We recognise the importance of this complex issue and are actively working with our suppliers to find sustainable sources of palm oil. As a result of this work we expect to make significant progress in the next 12 - 18 months."