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There are two methods I use for young puppies, which may work on your pup. I first try lubricating a rectal thermometer and take the puppies temperature. This frequently stimulates the puppy into going. If this fails and you have a nasal bulb syringe (aspirator), you can put warm water in it and gently squeeze a small amount into the rectum and see if this doesn't help.
At three weeks of age, I wouldn't feel comfortable doing much else. If that doesn't take care of the situation, I would have him seen by your vet.
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Just to followup and see how the little one is doing? Did you find my answer helpful? With weaning you are liable to see more of the pups having difficulty defecating.