The Change4Life campaign encourages parents to "Look for 100 calorie snacks, two a day max", to help them offer healthier snacks to tackle the obesity epidemic that is seeing a third of children leave primary school overweight or obese.
Eating disorder charity Beat said it was important that messages aimed at reducing obesity considered the impact they may have on those at risk of developing an eating disorder.
A spokesman said in a statement: "We have heard from parents and treatment providers who cite the promotion of anti-obesity messages to children as a factor in the onset and maintenance of eating disorders.
"Public health professionals must consider the wider impact of their campaigns, including the potential impact on mental health.
"We have heard from our service users who are concerned that this campaign may increase the risk of young people developing an eating disorder."
It added that while the Public Health England (PHE) campaign was aimed at parents, it was also likely to engage a younger audience and encouraging excessive focus on calorie counting could be harmful for young people susceptible to disordered eating.
The charity pointed out that the number of calories in a snack was not a reliable indicator of its impact on health, as for instance, a 100 calorie drink or snack with high levels of processed sugar was very unhealthy and would not reduce hunger, whereas many healthy snacks were more than 100 calories and could play an important role in a healthy and balanced diet.
"Focusing on calories rather than on healthy and balanced eating is unhelpful," the statement added.
"We encourage Public Health England to listen to concerns about the impact this campaign could have on those at risk of developing an eating disorder and change the campaign to focus more on healthy eating rather than calorie counting."
An online petition against the campaign has attracted more than 4,000 signatures.
PHE's chief nutritionist Dr Alison Tedstone said: "Our Change4Life campaign helps millions of families make healthier choices. Every campaign encourages families to eat more fruit and vegetables and use front of the pack labelling to choose healthier foods.
"This campaign responds directly to parents' concerns and our campaigns are rigorously tested with parents to ensure they provide helpful and practical advice.
"It's not about counting calories, it's a simple tip for parents to help change their children's snacking habits."