Police in the Philippine capital arrested more than 200 people during clashes with masked protesters that erupted on a day of largely peaceful anti-corruption demonstrations, a spokeswoman said on Monday.

At least 88 minors were among the initial count of 216 taken into custody on Sunday as police deployed water cannon and deafening sirens against crowds of mostly young, rock-throwing protesters.

Manila City mayor Isko Morena said a 12-year-old boy was the youngest detained.

Thousands 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.

The scandal has seen numerous lawmakers implicated and the leaders of both houses of Congress step down from their positions during an investigation.

But Sunday's street battles, which saw multiple police vehicles set ablaze and the windows of a precinct headquarters shattered, threatened to overshadow demonstrations that had been filled with families, activists, clergy and politicians.

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

"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 on Monday by the department of health, about 50 people were brought to a single Manila hospital following the clashes.

Another police spokesman, Major Philipp Ines, said 93 officers had been injured on Sunday, while adding the number of arrested could yet rise as people were still being processed.

Rage over the so-called ghost infrastructure projects has been mounting in the Southeast Asian country since President Ferdinand Marcos Jr 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 from 2023 to 2025 due to corruption in flood-control projects.

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

The protests came amid expectations of heavy flooding once more from Super Typhoon Ragasa. (AFP)