Abe is on a two-day trip to Israel and the Palestinian Authority.
The Iranian nuclear deal, he continued, is a bad agreement based on Iranian lies and deceit.
"Iran kept all the (nuclear) plans. Those who do not want nuclear weapons do not make plans and certainly do not keep them", PM Netanyahu told PM Abe, according to the PMO statement. Prime Minister will come back to Japan in the near future.
Palestinian president Mahmoud Abbas met Abe on Tuesday as part of the Japanese his Middle East tour, before which he has pledged "constructive" work on Israeli-Palestinian peace.
The meetings made Abe the first leader of a major country to visit both Israel and the Palestinian territories since Trump's controversial announcement in December that Washington would recognize Jerusalem as Israel's capital.
Some observers had suggested that a Middle East visit would be a risky move politically, given the heightening tensions that exist ahead of the relocation of the U.S. Embassy in Israel from Tel Aviv to Jerusalem.
Israel also agreed to help Japan train cybersecurity experts.
The Japanese leader affirmed his country's support for a political process based on the principle of a two-state solution and its readiness to contribute to any effort to achieve peace, WAFA said.
Ties between Israel and Japan strengthened after the a bilateral investment protection agreement was signed in January 2017.
The prime minister also asked Abe to lift his foreign ministry's travel warning regarding flights to Israel.
Prime Minister Abe said he would like Netanyahu to visit Japan again, and that he brought a business delegation with him on his visit to Israel.
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".
Netanyahu said in a statement: "We see the tremendous growth in Japanese investments of Israel, Israeli investments in Japan, the technology opportunities".