Stressing that the recent elections and its outcome would be written in golden words in the history of Nepal, the Indian Prime Minister said India-Nepal relations are special and "I visit at a special time".
He made the comments after the delegation talks with his Nepali counterpart K.P. Oli.
"India stands shoulder to shoulder with the people of Nepal, India-Nepal relations are about government relations, it's more like a family," Modi said.
"I, the Indian Government and the Indian people cordially congratulate the Nepalese people for the progress made under federal democratic construction."
In order to reach the new Communist government in Nepal, Modi held in-depth talks with his counterpart and high-level government officials to improve bilateral relations to be postponed following New Delhi's repeated attempt to cultivate Oli-led government Nepal in the last few months.
After the talks, Modi and Oli categorically gained some understanding.
In just two months, Oli met Oli twice, reassuring him that all serious and necessary grievances in Nepal would be addressed in a timely manner.
In this regard, Nepal and India achieved half a dozen important insights during the two-day state visit to Modi, which is expected to provide momentum in bilateral relations in the future.
However, India was silent on the exchange of banned Indian banknotes parked in various financial and banking institutions and held by the people, and on Nepal's request to add four additional air routes through India.
Modi and Oli held one-on-one interviews and delegation-level talks in which both sides agreed before September 1
India is ready to partner with Nepal on cross-border connections and agreed to conduct a survey to link Katmandu to Indian Railways investigation.
A team of India experts will begin the Rail Link Realizability Survey and India will send a team of experts to carry out the Inland Navigation Feasibility Study from Nepal to India.
"We are connected to Nepal by rail, water, transmission line, oil pipeline," Modi told the media.
He also announced a gift from the indigenous native radiotherapy machine for Bhaktapur-based cancer clinic.
Both sides agreed to send a joint technical team to solve the recurrent flood problem along the Nepal-India border.
Both Prime Ministers agreed to expand cooperation in agriculture. The first meeting of Ministers of Agriculture from Nepal and India will be held soon to develop a roadmap for agricultural research and development, education and organic farming.
The two heads of state also agreed on an early meeting for the construction of the 4,600 MW Pancheshwor Multipurpose Project jointly by India and Nepal.
"We have evaluated the partnership between Nepal and India, some of the projects have progressed and some are making good progress and we have agreed to fully review the trade and transit agreement," said Modi.
"We connect waterways, railways, roads, pipelines and oil pipelines and work together in areas of safety and defense."
The highly anticipated 900-megawatt Arun III hydropower plant was inaugurated during a joint press conference at Hotel Dwarika's in the capital Battisputali.
The Investment Board Nepal (IBN) issued a power generation license to generate power from the Arun III project in eastern Nepal on Thursday to the SJVN Arun III Power Development Company.
Earlier in the day, Modi was assigned the honor guard for a ceremonial function in the Nepal Army Pavilion. The Nepalese Army cannon offered a salute with 21 shots in honor of the Indian Prime Minister.