Though veterinarians and bovine farmers point to the effectiveness of transfaunation for treating digestive disease, many animal rights groups argue that the practice is unnecessarily harmful to the quality of life of the cannulated cow. Use of a rumen-fluid collector instead of fistulation is well tolerated by the donor cow. People for the Ethical Treatment of Animals points to the surgerys four- to six-week recovery period and suggests that arguments for the health benefits of cannulation obscure the profit motive of the dairy industry: "While some claim that this transfer can improve the health of cows, the procedure seems mostly to benefit the meat and dairy industries bottom lines—optimizing food and digestion for animals who will ultimately be exploited and slaughtered." Similarly, The New Zealand Anti-Vivisection Society describes the practice as "cruel, insensitive and barbaric [...] the epitome of using cows as mere objects, like cars with gas tanks."
The fact-checking site Snopes has determined that the description of a circulating video of a cannulated cow as "abuse" is a "miscategorization," saying that cannulation "is neither a form of abuse nor a method to increase dairy production." However, rumen cannulation has long been used by the dairy industry to study methods that improve milk production. For instance, a 1940 study used cannulated cows to determine that a vitamin-rich diet makes for more antiscorbutic milk than a vitamin-poor diet, and a 2004 study used cannulated cows to evaluate treatments for a pH imbalance called subacute ruminal acidosis that is of concern to dairy farmers primarily because it damages milk production.