Earlier in the day, Modi held talks with Xi at Taj Fisherman's Cove in Kovalam where they chose to "manage their differences prudently" and "will not let them become disputes".
The two leaders started the second day of the summit with one-to-one talks which lasted for over an hour.
Answering questions at a press conference, Foreign Secretary Vijay Gokhale said, the Chinese President, however, briefed PM Modi on the visit of Pakistan Prime Minister Imran Khan to his country lately.
Delhi feels Beijing has broken an understanding to be aware of each nation's "sensitivities and concerns", the paper said, noting India had stayed silent over months-long pro-democracy protests in Hong Kong.
That will always colour China's actions vis-a-vis India because they are practitioners of realpolitik. Wuhan spirit has given our ties a new momentum and trust. And that is the real reason why Modi and Xi should continue to meet in these informal settings where, whatever else, the two sides can understand each other better, red lines are clearer and potential areas of cooperation, however narrow, can be identified. The two leaders spent five hours of "quality time". Earlier, Modi and Xi came together to the venue in a golf cart.
The August 5 revocation means that India's Jammu and Kashmir will be largely run by the central government as territorial autonomy has largely vanished. He held a one-on-one discussion with Modi on various issues in the coastal historic city of Mamallapuram.
The meeting at the magnificent Shore temple complex under a sea-facing colourful tent went beyond the scheduled time as both leaders touched upon a range of issues over sumptuous local delicacies.
Both the leaders have chose to establish a High-Level Economic and Trade Dialogue mechanism to better balance trade between the two countries.
"We must hold the rudder and steer the course of China-India relations, map out a hundred-year plan for the relations from a strategic and long-term perspective, inject a strong endogenous impetus into bilateral relations, and work together to realize the great rejuvenation of our two great civilizations", said the Chinese president.
Fourth, China and India should deepen pragmatic cooperation and tighten ties of interests, Xi said. The Prime Minister said that, in the Wuhan Summit, both the countries decided not to allow any differences to become disputes and be prudently managed. The first one was held in Wuhan, China a year ago.
Mr. Xi pointed out that both countries, neighbours important to each other, "are the only two major countries with over 1 billion people". On India's complaint of trade deficit which mounted to over $57 billion a year ago in over $95 billion of total trade, Xi said, "We should take the establishment of the high-level economic and trade dialogue as an opportunity to synergise our economic development strategies and explore the establishment of a manufacturing partnership". "Today, our Chennai vision will begin a new age in relations between our two countries". Xi and his delegation's attention this weekend was divided between Modi and Washington, where China's chief negotiator, Liu He, met his United States counterparts to achieve a bare-bones trade agreement.
The two leaders agreed that China and India should respect and learn from each other so as to jointly achieve common development and prosperity, as well as the great rejuvenation of the two civilizations, it said.
Modi launched a "Clean India" campaign after he became prime minister in 2014. The comments evoked sharp reaction from New Delhi.
"There is a new focus on people to people connect between the two countries", he added. The Wuhan summit had led to "healthy and steady development" in ties.