Mr Patrick Gerard Donnelly (61), of Cabra, Irvinestown, Enniskillen, was convicted at Enniskillen Magistrates' Court on Monday, 20 June 2016.
Mr Donnelly pleaded guilty to both charges and received two months imprisonment on each charge, to run simultaneously, plus £28 costs.
This case arose from an anonymous complaint, in 2015, to the then Department of Agriculture and Rural Development (DARD), now DAERA, Department of Agriculture, Environment and Rural Affairs.
Commenting on the case, the Department said it "gives high priority to the welfare of animals and operates a vigorous enforcement policy to ensure full compliance of regulatory requirements.
"Any breaches are investigated thoroughly and offenders prosecuted as necessary," it said.
Offering advice relative to the case to other farmers, the Department added that it would be regarded "as good practice to remove, without delay, an animal carcase from a farm to prevent spread of disease and protect public health and avoid detrimental effects to the environment".
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