The 17-year-old boy was arrested and charged with alleged reckless conduct after one of the flares was set off on North Berwick beach.
Police said a group of youths had arrived in the town on Saturday and during their visit six flares were stolen from a boat. Five of these were buried in the sand, while one was set off.
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Hide AdPolice and coastguard attended and recovered three of the buried flares. However, two remain unaccounted for.
A police spokesman said: “Flares are an essential tool for alerting maritime officials to persons in danger while at sea. They are not toys.
“Officers will continue to search for the missing flares.”