Secretary of State Henry A. Kissinger, in an extraordinarily emotional farewell to American Jewish leaders, said yesterday he had never forgotten his own Jewishness during the years of negotiation over a Middle East peace settlement.

"I have never forgotten that 13 members of my family died in concentration camps," he told a luncheon in his honor sponsored by the Conference of Presidents of Major American Jewish Organizations. "Nor could I ever fail to remember what it was like to live in Nazi Germany as a member of a persecuted minority."

As a result, Kissinger asserted in an off-the-cuff statement that he said "comes from the heart," he believes "it is not compatible with the moral conscience of mankind to permit Israel to live a ghetto existence in the Middle East similar to the suffered by individual Jews in a number of countries over the centuries."

However, he said, it was important for American Jews that actions of the first Jewish Secretary of State in support of Israel "reflected not my personal preferences but the basic interests of the United States."

Kinssinger's uncharacteristically emotional references to his own past as a Jew who fled Germany in the '30s were echoed in the tributes paid to him by the American Jewish leaders at the lunch, where he received a gift set of the Encyclopedia Judaica.

"We pay tribute," said Rabbi Alexander Schindler, head of the umbrella organizations, "because we sense in his depths a commitment to Israel and the Jewish people. He may have been objective, but he was never detached."

Both the Jewish leaders and Israeli Ambassador Simcha Dinitz referred to "tactical differences they had had with Kissinger. Some elements within the Jewish community boycotted the luncheon, and two radical organizations outside the Jewish establishment - the Jewish Defense League and SOIL (Save Our Israel Land) - picketed the hotel and distributed leaflets charging that Kissinger is an enemy of Israel.

Kissinger said that "no critism has hurt me more" than that from the American Jewish community.

"I like to believe," Kissinger said, "that our disagrements never went to the heart of the relationships, that they concerned tactics to achieve a mutual objective," He defined basic American policy as insuring Israel the strength to make its choices freely and not have "decisions imposed by outside factors or by its neighbors."

Kissinger also defended his step-by-step negotiations after the 1973 Arab-Israeli war. He argued that "at attempt to solve everything at once would have involved risks of catastrophe too profound for any statesman to attempt."

He told the Jewish leaders that he would remain dedicated to them and to Israel "as long as I live."