The ecosan approach has been criticized for being overly focused on reuse in agriculture, whilst neglecting some of the other criteria for sustainable sanitation. In fact, ecosan systems can be "unsustainable", for example, if there is too little user acceptance or if the costs of the system are too high for a given target group of users, making the system financially unsustainable in the longer term.
Some proponents of ecosan have been criticized as being too dogmatic, with an over-emphasis on environmental resource protection rather than a focus on public health protection and provision of sanitation at a very low cost (for example UDDTs, which some people call "ecosan toilets", may be more expensive to build than pit latrines, even if in the longer term they are cheaper to maintain).
The safety of ecosan systems in terms of pathogen destruction during the various treatment processes is a continuous topic of debate between proponents and opponents of ecosan systems. However, the publication of the WHO Guidelines on Reuse, with its multiple barrier concept, has gone a long way in establishing a common framework for safe reuse. Nevertheless, the question remains whether ecosan systems can ever be scaled up to reach millions of people and how they can be made sufficiently safe to operate. The initial excitement in the early 2000s by the ecosan pioneers has changed into a realization that changing attitudes and behaviors in sanitation takes a lot of patience.
Acknowledgement for ecosan came with the awarding of the Stockholm Water Prize in 2013 to Peter Morgan, a pioneer of handpumps and ventilated pit latrines (VIPs) in addition to ecosan-type toilets (the Arborloo, the Skyloo and the Fossa alterna). Peter Morgan is renowned as one of the leading creators and proponents of ecological sanitation solutions, which enable the safe reuse of human excreta to enhance soil quality and crop production. His ecosan-type toilets are now in use in countries across the globe, centred on converting a sanitary problem into a productive resource.
Also many of the research projects that the Bill and Melinda Gates Foundation have been funding since about 2011 in sanitation are dealing with resource recovery – this might well be a legacy of the ecosan concept, even if the term "ecosan" is not used by these researchers.