At least 88 minors were among those taken into custody as police deployed water cannon and deafening sirens against crowds of mostly young, rock-throwing protesters.

Manila City Mayor Isko Moreno said a 12-year-old boy was the youngest detained on Sunday. Michelle Blanco told AFP her son Zoren was 13.

Standing in a line outside the Manila Police District offices, the 45-year-old saleswoman said she hadn't been told when her son would be released despite having spent most of the day there.

"A little information about how they are doing inside or what we should do to get him out means a lot," she said, insisting her son had only been watching when scooped off the street.

Elsie Santos said her son Reden had a speech impediment, showing AFP journalists the 27-year-old's PWD, or person with disability, card.

"No one is explaining anything to us at this point," she said as a small group of youth activists chanted for the prisoners' release in the background.

"My son cannot communicate properly, and I'm scared they won't understand him when he explains himself."

- 'Maximum tolerance' -

Thousands of Filipinos rallied in Manila on Sunday to vent their anger over a ballooning scandal involving bogus flood-control projects believed to have cost taxpayers billions of dollars.

But peaceful demonstrations filled with families, activists and clergy were later overshadowed by street battles that saw police vehicles set ablaze and the windows of a precinct headquarters shattered.

"So far, none of them are saying the reasons behind their actions or if somebody paid them to do it," regional police spokesperson Major Hazel Asilo said of those arrested.

"As soon as we know their affiliations, we can know if they were part of the protesters or if they were just causing trouble," she added.

According to a statement released Monday by the department of health, about 50 people were taken to one Manila hospital alone following the clashes.

Police said 93 officers were injured in the melees.

Amid accusations by at least one local rights group that police had used disproportionate force, interior secretary Jonvic Remulla said their response had been one of "maximum tolerance".

"They only had their riot gear and no firearms," he said of the 4,000 police deployed, noting that no weapons had been discharged or tear gas fired.

Rage over 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.

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.