The animals were seized from a farm in Co Kilkenny following concerns for their welfare, as well as other issues including legal ownership.
A spokesperson said the decision follows several weeks of discussions involving the Gardai, the ISPCA and the Irish Horse Welfare Trust.
The Department says some of the animals are healthy but the welfare of all the horses was under threat for some time.
Twenty horses - including a pregnant mare - will stay with the Irish Horse Welfare Trust and be re-homed, as agreed.
However, the IHWT have said say they want to try to save more of the animals, claiming they are quality horses and should not be sent to slaughter.
The Department of Agriculture would not disclose the location of the slaughter plant.
