“It is a sad day for the country,” he said.
“We’ve had a great year but the future looks very dark.”
Mr Kelly, who was speaking at the annual conference of the Irish Society for the Prevention of Cruelty to Animals, was speaking as Ireland has begun to re-establish itself as a global leader in animal welfare.
“Ireland has a lot of work to do and we will continue to be the leader,” he added.
“But I am very confident that we will be able to pull ourselves together and turn the tide.”
A number of issues, including the issue of euthanasia, are under consideration, he said, including a plan to increase the number of animals in foster care.
“It’s the first step to having a fully-fledged social housing network,” he told the conference.
Mr Kelly said the plan was to be announced this week.
The plan will include the creation of an animal welfare board.
The move comes as Ireland continues to grapple with the fallout from the botched horsemeat scandal.
The scandal led to the resignation of the Health Minister, Mary Mitchell O’Connor, and brought down the Taoiseach, Enda Kenny.
It also led to an international outcry and calls for a boycott of Irish meat.
The Irish Government is currently reviewing the policy for the sale of meat to slaughterhouses.