The protesters, composed mostly of workers, students, business, and religious groups, braved intermittent rains to push for Estrada's ousting ahead of the impeachment trial expected to start as early as December 4.
The mounting calls for Estrada's resignation started last month when an estranged friend accused the president of collecting more than eight million dollars in illegal gambling payoffs and pocketing 2.6 million dollars in tobacco taxes.
Estrada, the first Asian leader to be impeached, denied the accusations and vowed to answer the charges that included bribery, graft and corruption, betrayal of public trust, and violations of the constitution.
The chief executive appealed to the people to unite behind his effort to improve the quality of lives of the millions of impoverished.
"I call on all Filipinos - farmers, fishermen, urban poor, workers, teachers, and civil servants - let us intensify our efforts to build the nation," Estrada said in a statement a day after arriving from Singapore summit with fellow southeast Asian leaders.
"I have been doing everything to address the problem of poverty," Estrada added. "But I cannot do it alone. I need your help."
The protesters insisted Estrada should quit immediately since he has become a lame duck president.
"Estrada should no longer wait for the outcome of the trial because he can no longer govern effectively," said Ed Legaspi, a non- government organization worker.
Legaspi warned that Estrada's continuous stay in power could only lead to more misery for the country, including a looming economic recession.
"We pray that President Estrada would gain enlightenment and realize that the best he could do for the country is to step down immediately," said former securities chief Perfecto Yasay.
The rally kicked off a week-long series of protests against Estrada's continued stay in power that would include work stoppages, transport strikes, and more rallies.
Chief Superintendent Edgardo Aglipay, head of the Metropolitan Manila police force, appealed to opposition leaders to watch their ranks closely against saboteurs.
Aglipay said they gathered intelligence reports that armed communist rebels were already in the city to foment disorder during the protests.
Opposition Senator Teofisto Guingona said he received reports that allies of the embattled chief executive have brought to Manila members of a notorious crime syndicate in the southern region to sow disorder during the protests.
"I have alerted our security people to find out if this is true," Guingona said in a radio interview. "I am against trouble-makers joining the ranks of (legitimate) protesters."
Eddie Villanueva, leader of a religious group that led Sunday's protest rally, said Estrada has to step down immediately since he already lost the moral authority to govern.
Presidential Spokesman Ricardo Puno warned the protesters against "consorting with groups known for their dangerous and discredited ideologies".
"They should be careful," Puno said. "I think it is obvious that groups with discredited ideologies have infiltrated their camp and these groups don't have the people's welfare in their mind."
On Friday, a suspected communist rebel slipped past the tight security of the presidential palace and threatened to explode an incendiary bomb before the guards subdued him.
(dpa)