The Irish Cooperative Organisation Society says there would have been "serious animal welfare issues" if marts were not reopened.
The Department of Agriculture announced yesterday that marts can now provide essential services.
However, normal auction activity will not resume until further notice.
Ray Doyle from ICOS says the facilities need to be in operation.
"There's roughly 3.5m sheep born every year in Ireland, 2.5m dairy calves born, 1m suckling calves born.
"These animals have to be traded, they have to find new homes.
"You would have had serious animal welfare issues if the mart was not reopened for this."
