Assuming you have an account with FedEx and UPS do this -- contact your account representative and have them send you their food safety (related) guidelines in how MARKED boxes of food products are shipped.
The guidelines will explain in detail what steps they take to "ensure" that your boxes containing food are not shipped together with items that may be counter (such as chemicals) to food.
They have these guidelines because they both operate custom logistic operations for a number of food companies.
There will be markings that you need to put on your shipment boxes as alerts to keep your boxes away from those that would cause issues.
With all that said there is also the good possibility that your box will be sitting next to a box of chemicals, etc - so design your shippers for the worst possible handling and shipping situation.
Outside of our SQF consulting business I am co-owner in a logistics business and we routinely ship coffee and normally by DHL and FedEX. We use their shippers, but declarations as to content are on the outside of the box with standard wording to keep our packages away from chemical agents.
Let's face it, have you ever looked inside a supermarket chains DC trailers and noticed how they protect food products going to their markets and their customers, it is full allergen city, batteries on top of the boxes of strawberries, lawn spray under the cans of peanuts and fresh fish under ice next to the boxes of candy bars.
So what it all boils down to is package up your products very well and include tamper proofing, declarations galore on the outside might help too.
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