Trump said the United States supported efforts to end the violence, to ensure accountability for atrocities committed, and to facilitate the safe and voluntary return of the refugees.
Trump's first official visit to the region was billed as a push to step up worldwide pressure on North Korea over its nuclear weapons program and reduce USA trade deficits with South Korea, Japan and China.
Retno Marsudi, Indonesia's foreign minister who was present at the meeting, revealed that member states "condemned North Korea's ongoing development" of nuclear and ballistic missile capabilities, and said that their nuclear tests were "a threat to the region's peace and stability".
Reporters tried to query whether Trump had raised the issue of human rights with Duterte.
However, Annelise Riles, a professor of far east legal studies and anthropology at Cornell University, said Trump did not fulfil his agenda in Asia.
He says, "We've made some very big steps with regard to trade-far bigger than anything you know", in addition to business deals forged between USA and foreign companies.
Protesters burned an effigy of Trump on Monday.
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Earlier, as regional leaders gathered at a colorful ceremony to open the summit in Manila, Duterte sidestepped the controversy over his war on illegal drugs and its thousands of extrajudicial killings.
The East Asia Summit brought together the 10 members of the Association of Southeast Asian Nations, along with Japan, China, South Korea, Australia, New Zealand, India, the US and Russian Federation.
He tried to have it both ways on the issue of Russian interference in last year's presidential race, saying he believes both the US intelligence agencies when they say Russia meddled and Putin's sincerity in claiming that his country did not. Spokeswoman Sarah Huckabee Sanders said human rights came up "briefly" in the context of the Philippines' fight against illegal drugs.
Questions about Russian meddling in the 2016 election have followed President Donald Trump to Asia.
But Trump also says he believes Russian President Vladimir Putin when Putin claims his country did no such thing.
He does not blame other countries "for taking advantage of the United States on trade", Trump continued.
Trump is slated to attend a pair of worldwide summits and meet with Philippine President Rodrigo Duterte.