He met with Palestinian President Mahmoud Abbas the day before after arriving from Jordan.
But PM Abe said that Japan will continue to support it.
Some observers had suggested that a Middle East visit would be a unsafe move politically, given the heightening tensions that exist ahead of the relocation of the U.S. Embassy in Israel from Tel Aviv to Jerusalem.
During the trip, Abe secured visits with leaders from both Israel and the Palestinian Authority, a rare feat for a foreign leader of a major economy.
For the last four weeks, Gazans have staged mass rallies along the strip's eastern border to demand the "right of return" to their homes in historical Palestine from which they were driven in 1948 to make way for the new state of Israel.
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The Center for Constitutional Rights said in a statement Tuesday that the trip was created to help participants "better understand the human rights situation in Israel and Palestine, including the history of systematic displacement and institutional racism, as well as the work of human rights defenders there".
In an elaborate televised presentation on Monday, Israeli Prime Minister Benjamin Netanyahu revealed a massive trove of over 100,000 files obtained by Israel in a stunning intelligence operation. "We have seen tremendous growth in Japanese investments in Israel, Israeli investments in Japan, and of technological opportunities".
"I hope we will continue developing investments between our two countries", Abe said.
The Hebrew daily also said that the Japanese prime minister stressed his support for the two-state solution between Israel and the Palestinians, and told Netanyahu that Tokyo would not move its embassy to Jerusalem until final status issues are resolved.
The two state leaders agreed to move forward on the issue of direct flights from Japan to Israel, which would increase tourism, investments and business. He is accompanied by his wife and a delegation of senior Japanese business leaders.