With clenched fists in the air, the protesters chanted "Junk APEC", referring to the Asia-Pacific Economic Cooperation group of 21 economies whose leaders were meeting in Manila.
Police carrying wooden truncheons and shields fired water cannons at the protesters when they tried to break through barricades preventing anyone reaching the summit venue, about one kilometre (0.62 miles) away.
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The protesters said they opposed APEC's free-trade agenda because it favoured big corporations and neglected the poor.
"Aquino should protect his people, globalisation has caused the prices of our goods to go down. We barely break even," one of the protesters, 47-year-old rice farmer Nida Floresca, told AFP.
"We don't even have irrigation to water our crops. Aquino should think of us first."
Floresca came with several neighbours from their farming town in La Union around 270 kilometres north of Manila. They marched in sandals and straw hats.
One police officer estimated the crowd at about 2,000 although there were no official numbers given. There were no immediate reports of arrests or injuries.
More than 20,000 police and soldiers were deployed this week to ensure security during the APEC summit.
Philippine authorities said they had already been planning the nation's biggest ever security operation for the meeting, which was ratcheted up even higher after last week's terrorist attacks in Paris.
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