Funding for the 30 organisations was set to run out at the end of next month.
The last-minute reprieve affects groups including the Irish Heart Foundation, the Motor Neurone Disease Association, the Alzheimer's Society and the Irish Stammering Association which is chaired by Templemore native Michael Ryan.
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The new money will help support the groups up to the end of June 2016.
Environment Minister Alan Kelly and Minister of State for Rural Affairs Ann Phelan admitted that the withdrawal of funding for the groups would have made it very difficult for them to maintain their services.
But the organisations will still have to re-apply for the next round of funding, which begins in June 2016.
