The talks were held between Iran’s Foreign Ministry director general for human rights and women affairs Mansoureh Sharifi Sadr and her Japanese counterpart.
During the meeting, the two sides reviewed policies and actions undertaken in relations with the human rights and discussed issues of mutual concern.
They also exchanged views on ways of cooperating with the United Nations.
Experts from both countries had a separate session during which they discussed the judiciary systems in Iran and Japan.
The next round of talks is due for 2017 in Tokyo.