This will mark the second time that Modi will be hosting a visiting leader and holding bilateral talks in Gandhinagar - the last time was his meeting with Chinese President Xi Jinping in September 2014. Abe and Modi are also likely discuss the way ahead for strengthening defence ties between the two countries.
The two leaders and Japan's First Lady Akie Abe boarded an open jeep and proceeded from the airport to the historic Sabarmati Ashram with thousands of cheering people lining both sides of the eight-and-half km route.
The pact envisages the expansion of DAILAB - the laboratory set up by India's Department of Biotechnology and Japan's National Institute of Advanced Science and Technology.
In a first, Prime Minister Narendra Modi and his Japanese counterpart Shinzo Abe would take part in a road show in Ahmedabad in Gujarat on Wednesday when the latter begins his visit.
The leaders then headed to the nearby "Agashiye" restaurant for dinner in the old city area.
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Abe and Modi are also expected to exchange views on North Korea, which carried out its sixth and most powerful nuclear test on September 3 despite repeated warnings from the global community, according to Japanese government officials.
The next schedule of the two dignitaries would be the the 12th India-Japan Annual Summit at the sprawling auditorium complex Mahatma Mandir in state capital Gandhinagar.
The two-day visit of Abe beginning Wednesday afternoon, will also be marked by the Annual Bilateral Summit between Japan and India. During that visit, Japanese PM Shinzo Abe flew down to Kyoto to offer a warm welcome to our prime minister. Indian Prime Minister Narendra Modi will be laying stone to the prestigious project along with Japanese PM Shinzo Abe. The two nations had signed a deal for India's first bullet train in 2015. "A parallel CEO conference will also be held at the same venue, where representatives from both India and Japan will participate", the official said, adding that an entire hotel in western Ahmedabad has been booked to accommodate a Japanese delegation that will be arriving with Abe, the report added.
On Thursday, Mr. Modi and Mr. Abe will lay the foundation stone for the ambitious Ahmedabad-Mumbai high-speed train project to be built with almost 80% funding from Japan. To cover the stretch, a total of 12 stations have been proposed which will connect through Mumbai, Thane, Virar, Boisar, Vapi, Bilimora, Surat, Bharuch, Vadodara, Anand, Ahmedabad and Sabarmati.
"The Prime Minister of a country which as important as Japan, who is India's strategic partner in many respects, is strangely not even being hosted in Delhi".