Prior to their departure, Indian officials made it clear that Modi is expected to raise the exodus of the ethnic Rohingyas into neighbouring countries.
An online petition calling for the revocation of Myanmar State Counsellor Aung San Suu Kyi's 1991 Nobel Peace Prize has accrued 366,000 signatures, PressTV reported.
"I feel that India's democratic experience is relevant to Myanmar and therefore, in Myanmar's executive, legislature, election commission and press council are institutions where we have comprehensive cooperation programmes in capacity building", he stated, adding that as neighbours, both countries' security interests were the same.
India has also provided humanitarian relief following natural calamities like Cyclone Mora this year, Komen in 2015 and Nargis in 2008 and an quake in Shan state in 2010.
People cheer for PM Modi at Thuwunna Stadium in Yangon
The Myanmar's president Htin Kyaw and Suu Kyi had visited India past year.
India on Wednesday shared its concerns with Myanmar over the situation in the country's Rakhine state where the army has launched a crackdown on the Rohingyas, triggering a mass exodus.
■ Would like to thank India for taking a strong stand on the terror threat that Myanmar faced recently: State Counsellor Aung San Suu Kyi.
Ahead of his visit, Modi had said India and Myanmar were looking at strengthening existing cooperation in areas of security and counter-terrorism, trade and investment, infrastructure and energy, and culture.
Stating that people-to-people ties are the strength of India-Myanmar relations, he said that a road project connecting Manipur in northeastern India with Myanmar has been approved.
He said in future also India would take up projects that will be according to the needs and priorities of Myanmar. Thousands of Rohingyas are crossing over into Bangladesh and India to escape from the persecution in Rakhine.
PM addresses the Indian Community in Myanmar. When I am travelling, I make it a point to interact with the Indian diaspora, PM Modi said adding that the Indian diaspora has contributed to the development of wherever they have settled.
"We have pledged to build a new India by the time independent India turns 75 in 2022", he said.
In addition to these agreements, the initiative of building a hospital in Nay Payi Taw has been introduced in Modi's first bilateral visit to Myanmar.
Geographically, Myanmar is the first stop for India's Act East policy.
In Bagan city, Prime Minister Narendra Modi will be visiting the 1105 AD Ananda Temple which is another prominent Buddhist shrine in Myanmar. He had earlier to this country in 2014 to attend the Association of Southeast Asian Nations (Asean)-India Summit.