The protesters burned an effigy of an American eagle that resembled a vulture, as they gathered near a roadblock less than one kilometre from the summit meeting.
The demonstrators, from women's rights group Gabriela, were blocked from approaching the Philippine International Convention Center, where the leaders including U.S. President Barack Obama, Chinese President Xi Jinping, and Japanese Prime Minister Shinzo Abe held a closed-door meeting.
Police and soldiers equipped with anti-riot gear scuffled with around 200 demonstrators, who were chanting activist slogans and waving anti-APEC banners.
The demonstrators called on world leaders attending the summit to put a stop to pro-corporation and pro-rich economic policies.
"We just want to ask the world leaders of the APEC to put a stop to their meeting, because we know that what would actually follow is the plundering of our natural resources. What would follow are policies that will not be of help to the poorest of the poor," secretary-general of Gabriela, RJ Manalo, said.
Earlier on Thursday, security forces used water cannons to prevent hundreds of demonstrators from disrupting the summit.
APEC, which accounts for 60 percent of global output and nearly half of world trade, is aiming for a larger free-trade area for its 21 economies by 2025, but a re-emergence in some states of protectionism as growth stutters could be a hindrance.
Regional tensions over the South China Sea and security concerns after the attack by Islamist militants on Paris could eclipse efforts by Pacific-Rim leaders this week to boost trade and growth across a region of around three billion people.
Around 30,000 soldiers and police have been deployed in the Philippine capital to protect the leaders. Defense officials have said there has been no intelligence suggesting a major threat to the Manila summit.
The Philippine government declared a two-day holiday on November 18-19. Authorities have closed several roads and highway lanes for the exclusive use of delegates' vehicles to allow leaders to get to the meeting venues smoothly.
