The RSPCA response follows Five News' footage of a Freedom Food accredited farm.
In a press statement it said: "The RSPCA is angry and appalled that anyone would let animals get into this state, and we have immediately suspended the farm and launched a full investigation.
"The farmer's employer recognises there has been a serious breakdown of management on the farm. The farmer is currently battling with serious personal difficulties which appear to have overwhelmed him, however this is no excuse for the condition of some of the animals."
It added: "In rare cases individual farms or farmers can let us down, but for every animal shown on covertly-filmed video, there are millions more who've had a better life, thanks to the RSPCA's welfare standards.
"Freedom Food has more monitoring visits and inspections than any other assurance scheme in this country. It is a mark of a good scheme that immediate action is taken if ever a problem arises, and that's what we have done."