The rallyists had earlier marched near the US embassy and were heading to the nearby Malacañang palace when riot police blocked their way and used their truncheons to break up the crowd.
Rally leaders said six protesters were arrested. At least one protester was seen injured.
The leftist Nationalist Alliance (Bayan) denounced the dispersal, saying it had been conducted in a "treacherous manner."
In a statement, the group charged the government of President Arroyo of using a "mailed-fist approach" to curb peaceful civilian protests.
The government has imposed a strict policy of banning street rallies held without permits following reports that such gatherings may be used to destabilize the Arroyo government and pave the way for a military takeover.
Leftist groups have been at the forefront of opposition to the WTO, demanding the withdrawal of the Philippines from the trade organization.
Yesterday’s rally was participated in by more than 2,000 farmers and fishermen who came from all over the country. Among others, they expressed strong dissent on the country’s participation in the WTO talks and demanded for the immediate resignation of Mrs. Arroyo.
"We (workers) can no longer bear the lack of progress in our agricultural industry, which Mrs. Arroyo has promised," said Sammy Malunes, national spokesman of Anakpawis, the umbrella organization of local agricultural workers.
"Government’s participation in Cancun will cause us further harm," he added.
Malunes said they were supposed to go to Malacañang after they consolidated their march, if only they weren’t dispersed by police.
The protesters went back to their station at the Philippine Independent Church in Taft Avenue after they were dispersed by the police. — With AP