The DSPCA says there is great difficulty in enforcing laws around the transportation and sale of puppies.
It comes after Ireland was designated a gateway for the multi-million euro black market of young dogs into Britain.
That's according to an investigation by the BBC's Spotlight programme in the UK.
Animal protection societies told the programme the illicit trade sees tens of thousands of dogs moved from the Republic of Ireland through Northern Ireland every year.
Mike Flynn, from the Scottish Society for Prevention of Cruelty to Animals (SSPCA), told the programme: "For the puppy trade in Scotland, I would say 90% of all problems come through Belfast.
"Considering last year we seized over 150 pups and at least 90% of them came over from Belfast.
"Whether they were bred in Northern Ireland or Southern Ireland, that is the route they came through," he said.
Gillian Bird is head of education and media at the DSPCA. She told Newstalk Breakfast this is an ongoing issue.
"It's not a surprise to us - it's something that we are aware of - it highlighted a lot more of it than I think anybody really understood.
"And some of the more ins and out of it - of the transportation, of the stopping in service stations and handing over puppies - it goes on, we know it goes on.
"But it's just such a difficult thing to actually stop and enforce the laws around it".
She says the neglected dogs are usually too young to travel.
"This is a situation of animals being over-bred, over-produced, coming from potentially unhealthy parents.
"Not necessarily living in particularly good conditions, and it's about them being transported when they're young, not getting vet checks.
"There's a whole clatter of things that are the issue here with that".
Dog Breeding Establishment Act
Gillian says current legislation is not helping the situation.
"Unfortunately in Ireland we have a thing called the Dog Breeding Establishment Act, where people can actually register themselves as breeders.
"And one of the issues that the DSCPA and the Irish Kennel Club have is the fact that there is no capping on the number of dogs that can actually be registered.
"If you can prove that you can adequately look after 400 or 500 breeding female dogs, they will issue you with a licence for it.
"And who in their right mind can actually look after that amount of female dogs and their puppies properly and adequately?
"These are not farm animals, these are animals that have been bred to be domestic pets - they should not be farmed in this way".
Anyone thinking of getting a dog should make their local rescue centre their "first port of call".
"You want to adopt an animal, you don't want to be buying it - because no matter how hard you try, people are getting conned into buying animals that are mass produced", she adds.