During the talks, Li stressed China's support for the economic integration of East Asia and the centrality of the Association of Southeast Asian Nations (ASEAN) in regional cooperation.
Trump is not at the Singapore summit, nor will he attend a subsequent gathering of world leaders in Papua New Guinea at the end of the week, having sent Vice President Mike Pence instead.
The atmosphere between Myanmar's leader, Aung San Suu Kyi, and Malaysian Prime Minister Mahathir Mohamed appeared frosty after Mahathir lambasted Suu Kyi on Tuesday for her handling of the crisis that led to mass killings and the exodus of more than 700,000 Rohingya from Buddhist-majority Myanmar since August 2017.
"With the headwind of trade protectionism, free trade is facing some difficulties", Mr Li said.
Returning to the theme as the leaders sat down to dinner, he said: "Countries are becoming insular, retreating from multilateralism and globalization, which has been the cornerstone of ASEAN peace and stability".
"Free trade has, in some aspects, prevented war effectively", he said in a speech on Tuesday.
China and Asean already have a non-binding "declaration" for the waterway but are working towards a more robust agreement.
Markets Right Now: Tech weakness weighs on stock market
Tuesday's moves come after the Dow dropped 602 points on Monday as Apple shares dropped on expectations of slowing iPhone sales. Shares of Apple fell 0.4 percent, breaking below its 200-day moving average, a key technical level watched by investors.
Such negotiations should be held without the United States and its allies, which fuel tensions by conducting "freedom of navigation exercises", according to Duterte.
The draft of a statement to be issued by RCEP nations later in the week, which was reviewed by Reuters, said the group would instruct "ministers and negotiators to work toward the full conclusion of the RCEP negotiations in 2019".
And since the Philippines is the country coordinator of the ASEAN-China dialogue relations from 2018 to 2021, Heydarian said, "It doesn't reflect well on the Philippines given we are that ASEAN-China country coordinate for next two years, which means we handle all crucial engagements between two sides, that's 11 countries".
In recent years, however, China has dragged its feet in the code of conduct negotiations, while changing the facts on the ground by reclaiming contested islands and now placing anti-missile systems on them. ASEAN nations have reportedly all submitted their official positions with regard to claims in the South China Sea. For years, they have been discussing a pact to prevent an escalation of disputes.
Asean's joint statement "emphasized the importance of non-militarization and self-restraint in the conduct of all activities by claimants and all other states" that "could further complicate the situation and escalate tensions in the South China Sea".
Back in 2015, Chinese President Xi Jinping reassured former US President Barack Obama at the White House's Rose Garden that Beijing would not militarize its then newly-built artificial islands in the South China Sea.
He cited, in particular, a long, drawn-out process to negotiate a "code of conduct" that Asean and China hope to conclude in three years.