I'll try this again -- did not mean to post that before I was done but I had to leave the computer for a bit and evidently hit reply....
You could try the USDA as most mills are licensed with the USDA. But I doubt anyone has those particular statistics because most puppymills and BYBs claim to be reputable breeders until they are caught in such blatant violations the law steps in and takes their dogs.
This site says APR is the most used puppymill registry:
Why Choose a COE Breeder? I have read some from their site before as I like the way they run the registration -- they register no dogs from pet stores, mills, etc...It is a closed registry. There are a few other dog breed clubs doing this as well but they seem to be the more rare breeds (Pointing Griffin for example). I would love to see the Yorkshire Terrier breed have a closed registry so that we could put some health restrictions on breeding.
I am going mostly on what I see and read. When I was allowing myself to go into pet stores that sold dogs & cats, I was seeing mostly ACA, APR and CKC here. Most of the YT members that have problems and find their dogs came from a mill, seem to say they are registered with non-AKC registries. Since the whole history of the other registries tells me the puppymills were their main founders -- stands to reason, most of them will be non-AKC. Although a great many operate with dual-registeries so that they can claim to be an AKC kennel, but they have the back up registery in case they get caught when DNA shows the wrong parents are listed on papers, or AKC inspections wind up banning them.
The AKC is also the only non-profit registery. (according to wikipedia). In 2006 they actually entered into a contract with Petland (supplied by the Hunte corporation -- biggest pet store supplier of puppies) but they bowed to the the instant disapproval of dog enthusiasts and rescinded that contract. So -- like I said, they are not perfect but since they are non-profit, they are more likely to bow out of the puppymill business than the other registries. Unfortunately, I am sure there are still plenty of mills using AKC dams & sires. But I think most of the worst offenders are being weeded out. They know that too -- that is why the border-line mills are using the double-registry trick to protect their backsides.
AKC is the biggest registry, so they still have a lot of AKC dogs in mills. I think the more notable numbers to look for would be the percentage of the registry that ARE puppymill and BYB dogs. We won't ever see those numbers in writing as most BYB claim they are not and even most puppymills like to try to pretend to be reputable breeders. So, it is something you have to gleen from talking with other pet owners and reading what is available -- mostly educated guesses. Maybe I should not have said most puppymill dogs are registered with one of the non-AKC registries but that most puppymills utilize a non-AKC registry. They may also have some AKC dogs -- but more than likely even those will have dual registration.
There are so many logical ways to see that AKC registration is preferable. For instance -- the offshoot registries will register any AKC registered dogs but the AKC will NOT register dogs from the other registries.
AKC has requirements for DNA testing when a dog is used a number of times in breeding -- the other registries have no such requirement.
AKC does not register dogs with photos, affadavits, or 2 vet letters -- they require AKC lineage. With other registries, it can be easy to get a mixed breed into their books as a purebred.
I have seen some beautiful dogs from non-AKC registries. But sometimes I wonder if those are the result of someone selling a dog with limited registration, and then the owner just circumvented the system and turned around and sent in for the non-AKC registration so they could breed even though the original seller had specifically NOT wanted that to happen. Some of those limited registration dogs may be carriers of genetic problems, faults, or the owner just did not want any Tom/Dick/Harry breeding their line. So that is one more reason against the non-AKC registries. I could probably keep typing reasons all night, but I am getting tired and need to get off here.