He flew in from Jordan to begin the final leg of a six-day tour of the Middle East aimed at promoting regional stability and peace as well as boosting economic ties.
Travelling with him is a 100-strong delegation of government officials and top business executives from Japanese firms which are world leaders in their field.
It is the first visit by a Japanese prime minister to Israel in nine years.
Abe, who was re-elected as premier last month, began his trip in Cairo where he pledged USD 2.5 billion in humanitarian and development aid for countries affected by violent expansion of the Islamic State (IS) jihadist group in Iraq and Syria.
Abe is expected to call on both Israel and the Palestinians to find a way to resume peace talks which collapsed nine months ago, the embassy said.
He was also to urge Israel to refrain from any actions or remarks which would escalate the confrontation with the Palestinians.
Abe's arrival comes just two days after the International Criminal Court said it would open a preliminary probe into possible Israeli war crimes following a complaint filed by the Palestinians.
Japan is a party to the court and also one of its biggest financial backers. Israel is also lobbying Canada over the ICC move in talks with visiting Foreign Minister John Baird.
"Netanyahu is expected to ask both Abe and Baird to take every measure possible to convey to the ICC the message that it is unacceptable to continue to single Israel out," said NRG, the website of Israel's Maariv newspaper.
On January 2, the Palestinians applied to become a party to the ICC in a process that will take effect in early April.
Last May, Netanyahu visited Japan for a five-day trip which was heavily focused on boosting the hi-tech trade between the two countries.
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