When I give flagyl for protozoans I just force feed the appropriate size piece of the pill. Usually when your giving flagyl the tortoise isn't eating and conversely not producing stool. If this vet won't prescribe it, I'd find another vet.
You will though have to replenish the good gut bacteria after you give the flagyl. Critical Care is very good for that, but you have to get it through your vet.

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