As of Friday, customers cannot order the marshmallow, graham-cracker and chocolate treat online, and supplies are extremely limited for Samoas.
It's uncertain when the products will be replenished.
According to the organization, leaders are asking their troops to take only what is needed and not overstock.
The six other cookie varieties are still widely available.
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Correction: A previous version of this story erroneously stated Orange County was also affected by supply chain disruptions. The story has since been updated.