The organization said on Thursday that energy drinks have been linked with cardiac arrhythmias, cramps, kidney failure, and even death.
It added that there was a particular danger of overdosing on stimulant chemicals with the shot-sized drinks, because they contain higher concentrations.
A 60-millilitre "energy shot"-sized can contain the same quantities of caffeine and taurin as a normal can of energy drink - but four times the concentration.
"Foodwatch is calling for a general ban on the sale of highly-concentrated shots," a statement on the organization's website said. "On top of that, normal energy drinks should include clear warnings on the packaging and should only be sold to over-18s."
Matthias Wolfschmidt, Foodwatch deputy chairman, said while the drinks represent a "huge business" for the drinks companies, "for the health of the customers it could be a huge danger."
Scientists have also warned of side effects "especially during sports or in combination with alcohol."