Various groups have protested in recent months following the discovery thousands of flood defence projects across one of the world's most typhoon-prone countries were substandard, incomplete or simply did not exist.
Government engineers, public works officials and construction company executives have testified under oath in hearings by the Senate and a fact-finding commission that members of Congress and officials at the Department of Public Works and Highways took kickbacks from construction companies to help them win lucrative contracts and avoid accountability.
Most denied the allegations.
About 650,000 members of the Iglesia Ni Cristo, or Church of Christ, joined the start of the three-day rally on Sunday in Manila's Rizal Park despite intermittent rains, police said.
Many wore white shirts and carried anti-corruption placards. About 2000 people, including retired generals, held a separate anti-corruption protest late on Sunday at the "People Power" monument in suburban Quezon city.
"These thieves have made us very outraged because we pay our taxes and these officials just plunder the treasury and rob us of our future," said Rachel Morte, a 41-year-old resident from northern Pampanga province who joined the huge Manila rally.
"We hope we'll get justice and the stolen money will be returned to the people."
Iglesia is an influential group that votes as a bloc and is courted by political candidates during elections.
The police, backed by the military, went on full alert and deployed thousands of personnel to secure the weekend rallies, which were peaceful, Interior Secretary Jonvic Remulla said.
During a September 21 anti-corruption demonstration, a few hundred black-clad protesters threw rocks, bottles and firebombs at police near the presidential palace in Manila, injuring more than 100 officers. Criminal complaints have been filed against 97 protesters.
The presidential palace went on security lockdown over the weekend, with major access roads barricaded by anti-riot police, cargo containers and barbed wires.Â
Flood control is an especially sensitive issue in the Philippines, one of the Asian countries most prone to deadly typhoons, flooding and extreme weather.
Two typhoons left at least 259 dead this month, mostly from flash floods and landslides, and affected millions of others.
President Ferdinand Marcos Jr has been trying to quell public outrage and street protests sparked by the scandal, saying on Thursday that many of the powerful senators, members of Congress and wealthy businesspeople who were implicated would be in jail by Christmas.
Marcos said an independent fact-finding commission he created has already filed criminal complaints for graft, corruption and plunder against 37 suspects.
Criminal complaints have also been filed against 86 construction company executives and nine government officials for allegedly evading nearly 9 billion pesos ($A233 million) in taxes.
