UPDATE: While on missions depending on the length of said mission a ninja would typically carry edemame (soy beans) and white rice. These would be pre-cooked so that the ninja had to do as little prep work on their mission. If on a full-night mission a ninja would possibly carry a vial of Panax Gensing extract for energy. The vials of gensing are now redaly available at health food stores and asian food stores or even your local supermarket in the vitamin isle. Remember that weight is always a factor in these situations and most of the time common sense and a knowledge of the foods of the era in Japan can help you find your answer.
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There is a story wich tells of a group of ninjas that had "hunger pills" that consisted of white rice and ginseng wrapped in nori that were soaked in Sake for three years. hope that helps.
Here's the answer. What'd ja think that ate?
i mean real ninjas
I don't think they ate anything when on a mission. They were so well trained that they lived off the energy inside their own bodies. If they carried any food it would have an odor that would betray their location since often times they were within 10 feet of the victim for hours or days at a time. Probably on the way back from a mission they ate what ever was at hand or could be gotten.