Rage over the so-called ghost infrastructure projects has been mounting in the Southeast Asian country since President Ferdinand Marcos put them centre stage in a July state of the nation address that followed weeks of deadly flooding.

Marcos had said early last week he did not blame people for protesting "one bit" while calling for demonstrations to remain peaceful. On Sunday they largely were.

But AFP journalists watched as groups of mostly young men threw rocks and bottles at police in two separate incidents, setting fire to the tyres of a trailer used as a barricade near a bridge leading to the presidential palace in one.

Police advancing behind a wall of shields arrested 17 mostly young people in the first encounter, local authorities said.

Barely an hour later, a second clash saw police use water cannon on another group of masked protesters. An AFP journalist at the scene saw some police pick up rocks and throw them back at the demonstrators..

It was not immediately clear if those involved had any connection to the organised protests.

The day began with a peaceful morning protest in the capital's Luneta Park that drew nearly 50,000 people, according to city estimates.

Thousands more joined an afternoon demonstration at the capital's EDSA thoroughfare, ground zero for the 1986 movement that ousted Marcos's dictator father.

"It's very rare for me to go to rallies, but this situation was bad enough that I was really urged to say 'this is enough'," Mitzi Bajet, a 30-year-old designer told AFP at the EDSA rally.

Teddy Casino, 56, chairman of left-wing alliance Bagong Alyansang Makabayan, said the group was demanding not only the return of stolen funds, but also prison time for those involved.

"Corruption requires people to go to the streets and express their outrage in the hope of pressuring government to actually do their jobs," he said.

- Millions lost -

The Department of Finance has estimated the Philippine economy lost up to 118.5 billion pesos ($2 billion) from 2023 to 2025 due to corruption in flood control projects.

Greenpeace has suggested the number is actually closer to $18 billion.

Earlier this month, the owners of a construction firm accused nearly 30 House members and Department of Public Works and Highways (DPWH) officials of taking cash payments.

The scandal has already sparked leadership changes in both houses of Congress, with House speaker Martin Romualdez, a cousin of Marcos, tendering his resignation earlier this week as an investigation got underway.

On Sunday, multiple politicians were among those taking part in the EDSA protest, an event supported by the powerful Catholic Church that drew numerous families.

"This is not partisan," said 58-year-old Manuel Dela Cerna, who said he had attended the People Power protests at EDSA four decades earlier.

"They are draining the people's money while citizens suffer from floods, their homes being swept away, while officials ride private planes, live in mansions," he said.

The Philippines has a long history of scandals involving public funds, in which high-ranking politicians found guilty of corruption have typically escaped serious jail time.