The herbicide, believed to be glyphosate, left schoolchildren who inhaled it vomiting and fainting, while others complained of stomach pains and headaches, a health official in the municipality of Nepena told journalists.
Glyphosate -- the active ingredient in US biotech giant Monsanto's Roundup weed-killer -- has often caused controversy and confusion.
Critics have called for it to be banned, and the World Health Organisation's International (AgFP) agency for Research on Cancer said last year that it "probably" causes cancer.
Parents complained to local prosecutors after their children got sick when the chemical was sprayed on sugar cane fields belonging to the Gloria group, one of the largest food and agriculture companies in Peru, said newspaper El Comercio.
The spraying was carried out Tuesday morning, apparently without a municipal permit, investigators told journalists.
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