In a joint statement, the two leaders said they would begin regular talks between their foreign and defense ministers and committed to extending cooperation in areas ranging from agriculture and digital technology to investment in Indian rail projects and infrastructure.
The two-day summit seeks to review the progress in ties and deepen strategic dimension of the bilateral relationship.
Both Modi and Abe called upon Pakistan to bring to justice the perpetrators of terrorist attacks, including those of November 2008 in Mumbai and January 2016 in Pathankot. Besides, India and Japan also made a decision to cooperate for the first time in Yoga and Ayurveda to provide holistic healthcare in both countries.
Experts said Abe, who last week became the first Japanese prime minister to visit Beijing since 2011, was performing a delicate balancing act - working to improve ties with China while keeping relations with India on a strong footing. The two leaders also affirmed that Asean unity and centrality are at the heart of the Indo-Pacific concept, which is inclusive and open to all.
Abe and Modi will hold a formal summit Monday in Tokyo, during which strengthening bilateral security and economic cooperation are expected to be high on the agenda. "A strong Japan benefits India and a strong India benefits Japan".
Modi and Abe said that there is a need for stronger global partnership in countering terrorism and violent extremism and called upon all countries to work towards rooting out terrorist safe havens and infrastructure, disrupting terrorist networks and financing channels, and halting cross-border movement of terrorists.
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Japan and China driven closer by trade tensions with US
The visit, which featured Japanese flags hung in the heart of Beijing, marks a dramatic outward improvement in ties from six years ago.
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By 2022, India's digital economy is expected to grow to United States dollars 1 trillion and lead to creation of 10 million jobs, according to consulting firm EY.
India, Japan, and China signed the currency agreement against the backdrop of trade tariff war initiated by the US President Donald Trump early this year.
On Sunday, Modi visited a factory operated by robot manufacturer Fanuc before being invited to Abe's vacation home near Mount Fuji.
PM Modi said Japan investors have announced they would invest $2.5 billion in India.
He also met Heita Kawakatsu, the Governor of Shizuoka province, and Yuji Kuroiwa, the Governor of Kanagawa Prefecture, and discussed ways to strengthen cultural and people-to-people ties between India and Japan.
PM Modi also lauded the Indian diaspora for introducing Kabbadi and Cricket in Japan where martial art is very popular. Japan is funding 80% of the Mumbai-Ahmedabad bullet train project through a soft loan of Rs 79,000 crore at an interest rate of 0.1%, with a tenure stretching over 50 years and a moratorium period of 15 years.