The Government has been criticised for its failure to help the thousands of women and girls across Europe who are under threat of female genital mutilation (FGM).
Colm O'Gorman, executive director of Amnesty International Ireland, claimed that during the first few months of the presidency it was not clear whether anyone in government knew which department was responsible for the area, with anti-FGM activists passed from minister to minister.
"The Irish presidency had a real chance to jump-start this and assist some of the thousands of women and girls across Europe who are under threat of FGM," he said.
"It is really disappointing that we saw no progress in tackling FGM in what was, otherwise, a positive presidency for human rights."
An estimated 180,000 girls and women in Europe are at risk of undergoing the procedure, either illegally in Europe or by being brought back to their parents' country of origin.
Another half a million in the EU - including 3,000 in Ireland - are believed to have already had FGM before leaving their home country.
Elsewhere, Amnesty's report card praised Ireland for taking significant steps to protect human rights during the EU presidency.
It highlighted efforts to keep negotiations of the anti-discrimination directive alive, and the push for further EU action to counter hate crime, racism, anti-Semitism and homophobia.
Mr O'Gorman said there were some big wins for human rights in Ireland's presidency.
"The Irish Government's emphasis on putting human rights at the heart of the EU's foreign policy was both significant and welcome," he said.
"The presidency played a positive role in ensuring a robust international Arms Trade Treaty was agreed at the start of April.
"The statement from the presidency on International Roma Day was a welcome demonstration of political support for Roma rights and there were strong new guidelines published on human rights for LGBTI persons."