Lee's comments confirmed earlier expectations that the 16 countries in the plan, called the Regional Comprehensive Economic Partnership, or RCEP, would not meet their goal of finalizing the accord this year.
The trade talks followed scores of bilateral meetings among the leaders and talks on other issues such as regional security, how to keep peace in the South China Sea and the crisis over hundreds of thousands of ethnic Rohingya Muslims who have fled to Bangladesh to escape violence in Myanmar.
During the meetings in Singapore, Lee has championed the region's commitment to free trade and a multilateral approach to sorting out the issue — in contrast with U.S. President Donald Trump's "American First" preference for bilateral trade deals and distrust of international institutions.
"We are meeting at a critical time. Protectionism and anti-globalization sentiments are on the rise. This can have a devastating impact on the regional as well as the global economy, and business confidence in Asia is already being affected," Lee said.
"It's important that we redouble our economic integration efforts and maintain a free, open and rules-based multilateral trading system which has underpinned our growth and prosperity," he said. Trump withdrew from a Pacific Rim trade initiative, the Trans-Pacific Partnership, just after taking office last year. That trade pact is due to take effect on Dec. 30. The U.S. is not part of the RCEP initiative, which includes China, India, Australia and most other Asian economies.
Lee said participating countries had finished seven of 18 chapters in their agreement and shown "strong political will" to finish it. He warned that further delays in reaching an agreement, already in negotiations for six years, would damage the RCEP's credibility.
"We are now at the final stage of negotiations. With a strong momentum generated this year, I am pleased to note that the RCEP negotiations are poised for conclusion in 2019," he said. The 10 Association of Southeast Asian Nations members are Brunei, Cambodia, Indonesia, Laos, Malaysia, Myanmar, the Philippines, Singapore, Thailand and Vietnam. Earlier Wednesday, the ASEAN leaders met with their counterparts from Australia, China, South Korea, Russia and Japan.
Managing conflict in the South China Sea is a perennial concern. China is pitted against its smaller neighbors in multiple disputes in the sea over coral reefs and lagoons in waters crucial for global commerce and rich in fish and potential oil and gas reserves.
While in Singapore, Chinese Premier Li Keqiang has sought to reassure China's neighbors. "We have found the way to properly manage and defuse differences, for example, on the issue of the South China Sea in the past years," Li said, adding that the situation was moving toward "greater stability" with progress toward a single draft text on a code of conduct in the sea. He reiterated Beijing's hope to have a final agreement within three years.
Philippine President Rodrigo Duterte said such a code is needed "at all cost" to prevent dangerous miscalculations. The Philippines softened its earlier harsh criticism of China's assertive moves in the disputed waters after Duterte sought to repair relations with Beijing once he took office in 2016 and sought infrastructure funding, trade and investment from Beijing.
The region already has a nonbinding "Declaration of Conduct" but is working toward a more robust agreement, with China appearing to win support for its calls to ban involvement by outside powers, such as the United States, in maritime disputes.
Duterte cited a risk of "serious miscalculation" and potential clashes that could trigger military action based on mutual defense treaties. "So you are there, so you are in possession, you have occupied it, but tell us what route we should take, what kind of behavior," he said.
"Everything's been excellent between China and the rest of ASEAN except for the fact that there's friction between the Western nations and China," Duterte told reporters as he headed into meetings. While the Singapore meetings were typically focused on cooperation and goodwill, concerns over Myanmar's treatment of its ethnic Rohingya Muslims flared with unusually sharp comments to the country's leader, Nobel Peace Prize laureate Aung San Suu Kyi.
U.S. Vice President Mike Pence told Suu Kyi on Wednesday that the situation was inexcusable. He also took aim at Myanmar's arrest and imprisonment of two Reuters journalists. On Tuesday, Malaysian Prime Minister Mahathir Mohamed lambasted Suu Kyi 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.
Mahathir, whose own country has a Muslim majority, said he told Suu Kyi that as a former political detainee, she should show more compassion. "They are actually oppressing these people to the point of, well, killing them, mass killing, and burial in graves dug by the victims and that kind of thing," said Mahathir, a 93-year-old political veteran whose own past treatment of dissidents at times drew opprobrium. "That may be relevant in ancient times, but in modern days, we don't do that kind of thing."