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"Vegan food is not recommended for young children," the office said. "It can cause serious harm."
The office said vitamin B12 is important to the brain, nervous system and the formation of blood.
The Schweiz am Sonntag newspaper said about a dozen Swiss children being fed vegan diets are treated for malnutrition each year.
Andrea Superti-Furga, professor of pediatrics at Lausanne's CHUV hospital, told the 20 Minutes newspaper newborn babies can also be negatively impacted by vegan mothers if their milk is low in vitamin B12.
"With vegans of a young age, a lack of vitamin B12 can lead to irreversible damage to the nervous system," Supert-Furga said.