Foreign Ministry spokesperson Emmanuel Nahshon said the meeting between retired Saudi general Anwar Eshki and ministry Director General Dore Gold took place at the prestigious King David hotel in west Jerusalem but did not give further details.
The Jerusalem Post newspaper said Eshki led a delegation of "businessmen and academics" on a mission to promote a stalled Saudi-led 2002 Arab peace initiative.
Top Arab diplomats vow to defeat 'terror'
It said that he met Major General Yoav Mordechai, head of the military body that coordinates Israeli activities in the West Bank and Gaza, and talked Friday in the West Bank to a group of Israeli opposition MPs.
Israel and Saudi Arabia have never had diplomatic relations but there have been media reports of intelligence-sharing in the face of shared concerns about Iran and the Islamic State group.
Eshki and Gold shared a platform in June last year at the Washington headquarters of the Council on Foreign Relations and "met to discuss opportunities and challenges in the Middle East," the council said on its website at the time.
"Their speeches focused on the danger Iran posed to their countries, and they revealed that they had been in secret discussions for a year, and had now decided to go public about their talks," it added.
Israeli army radio on Sunday aired an Arabic telephone interview with Eshki, chairman of the Jeddah-based Middle East Centre for Strategic and Legal Studies, in which he denied that his country had security links with the Jewish state.
Imminent threat against Americans in Saudi's Jeddah
"To my knowledge there is no cooperation in the struggle against terrorism," he said.
He said that Israel would only be able to make peace with the Arab world when it had resolved the conflict with the Palestinians, in accordance with the 2002 Arab proposal.
It calls for Israel to withdraw from the occupied territories and resolve the issue of refugees with the Palestinians, leading to the creation of a Palestinian state, in exchange for normalised relations with Arab countries.
"Peace will not come from Arab countries, but the Palestinians and the implementation of the Arab peace plan," Eshki said.
The radio quoted him as saying the Israeli-Palestinian conflict "is not the cause of terrorism, but it provides a breeding ground for conflict in the region." Egypt and Jordan are the only two Arab nations to have made peace with Israel.
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