Up to 30 lambs have been born each week in the urine and faeces infested saleyard pens or on crowded trucks travelling to yards.
The RSPCA, which struggles to find homes for them, predicts the problem will get worse during the next two months of the lambling season.
Both the RSPCA, and the Meat Industry Authority, which manages the salesyards,
bans the transport and sale of pregnant ewes.
Many sheep and other disabled and stressed animals which cannot be sold or fostered to volunteer carers are destroyed by RSPCA inspectors or saleyard workers.
RSPCA senior inspector Les Savill said sending pregnant ewes to the yards was cruel.
"It is blatently obvious when a ewe is pregnant and once sheep leave the farm they become our problem not the farmers," he said.
"I don't care what the farmers and saleyard workers think of me. I come from a farming background and I know it is not necessary to treat your animals like this."
Up to 30,000 sheep are transported to the saleyards in an average week from around WA, some travelling from as far away as the Kimberley.
But this week, because of the start of the lambing season, 90,000 sheep arrived and many newborn lambs and pregnant,crippled and blind sheep were left behind by truck drivers who refuse to transport the animals.
Meat Industry Authority chief executive Mike Donnelly said the authority and the RSPCA were left to resolve the problems caused by irresponsible farmers.
"We are always telling the producers not to send their pregnant ewes here.
They are not fit for transport in the first place and it is not pleasant for them if they lamb while on the truck,"Mr Donnelly said.
"In the case of pregnant ewes being brought to the yards, we are dealing with
the symptoms rather than the disease.
"Farmers who manage their focks properly might allow the odd pregnant sheep on the truck accidentally. However, when we get whole truckloads that are pregnant, as has happened before, that is outrageous."
Farmers who sent pregnant sheep to the saleyards risked prosecution.
Helena Valley volunteer animal carer Shirley Meggeson said emaciated and pregnant ewes were regularly taken to the saleyards.
WA Farmers Federation meat section vice-president Jim Alexander said the federation did not believe the problem was as serious as the RSPCA suggested.
"The industry has codes of practice on the way and is aware of its animal welfare responsibilities.If there is a member doing this then we don't want him associating with us," he said.