Micheal Mac Donncha participated in an Islamic conference about Jerusalem in Ramallah organised by the religious affairs adviser to Palestinian President Mahmoud Abbas.
The ministry said in a statement that Israel expresses its "deep disappointment and shock" over the incident.
Ireland's ambassador to Israel, Alison Kelly, was then called before the Foreign Ministry to explain the Lord Mayor's actions.
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A short while later Mr Mac Donncha announced that he was already in the Palestinian city of Ramallah, where he had been invited to attend a conference on the disputed status of Jerusalem.
It added that the Jewish state "expects a public and official Irish response to the conduct of the council of its capital city and particularly its head, who are conducting a campaign of discrimination and hatred against the state of Israel".
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Israel's Interior Ministry later admitted that the mayor had entered Israel "due to a typo".
Lord Mayor Mícheál Mac Donncha also hit out - saying it was disgraceful that some people had been stopped from entering the country to attend the conference in Palestine by Israeli officials.
Israel and Palestine are locked in a decades-long dispute over borders and sovereignty. Mac Donncha says he knows of no ban on him.
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