The protesters were expressing solidarity with a much larger crowd gathered in Makati that was calling for the resignation of President Arroyo in the wake of allegations she rigged last year's election.
The 10 children, aged seven to nine, were brought along by their mothers who were among the protesters.
They were hurt when police fired tear gas and water cannons to repulse and disperse the protesters who had stormed the building.
At least two firefighters, Ramon Molina and Roel Codoy, and one unidentified Air Force soldier were hurt in the ensuing melee. They suffered cuts and bruises on their faces and arms from stones and other projectiles hurled by the attackers.
Superintendent Mariano Natuel, who heads the police crowd control unit, said his men tried to exercise " maximum restraint " but had to use water cannons and tear gas when the protesters tore down the barricades protecting the building and stormed forward.
Kaira Alburo, one of the protest organizers, said at least 300 Cebuanos have also signed a manifesto calling for the resignation of Arroyo. The manifesto is intended to belie the notion that Cebu is solidly behind the president, she said.
Arroyo won by more than a million votes in Cebu over Fernando Poe, her closest rival in the May 2004 elections.
Cebu officials the other day signed their own manifesto expressing continued support for the president. They are also threatening to declare a separate Visayas republic in case Arroyo is forcibly removed from office.
A similar threat has been aired by officials in Mindanao.
Local officials around the country are largely supportive of Arroyo and there is growing resentment that national affairs are being dictated by a few thousand protesters in Manila.
A few hours after the violent protest at the Malacanang sa Sugbu was quelled, a pro-Arroyo rally of around 200 followers of evangelist Apollo Quiboloy was held at the Capitol.
In Makati, a much larger crowd of 30,000 according to official police estimates gathered to press the president to resign.
Troops and police, fearing the crowds would storm Malacanang or that communist rebels or Islamic militants may mount attacks under cover of the rally, went on full alert as early as the previous night, stopping convoys from southern and northern provinces that were on their way to join.
Waving a sea of banners, and chanting and singing protest songs, demonstrators brought the financial district to a standstill in the largest rally yet in the seven-week-old campaign to force Arroyo from office.
Massive army-backed revolts had already toppled two presidents, Ferdinand Marcos and Joseph Estrada, 1986 and 2001.
Yesterday, the supporters of Estrada and Susan Roces, the widow of Poe, who died of natural causes after his losing electoral bid, were among those in the rally.
A poll of 300 respondents in Manila showed 80 percent believe Arroyo was involved in poll fraud and 58 percent think she should resign.
But Arroyo has clung tenaciously despite the resignation of 10 of her top officials last Friday. She received crucial backing from ex-president Fidel Ramos, a former general who still wields influence over the military, which has pledged to stay neutral. The powerful Catholic church, which backed the earlier revolts, also refused to join calls for her resignation.
Not everybody who joined the rally, however, really cared about what the rally was for. One vendor, while saying she did not like the president, admitted she and many others like her had no choice but to join.
" We all have to attend. They ( Makati officials ) take our attendance. If we don't attend, we could lose our vending slots. "
The biggest draw had not been a sincere desire to force Arroyo out but the movie stars and musicians that kept the crowd rocking.
To the tune of the Beatles' " Don't Let Me Down, " the crowds sang " Gloria Step Down. "
The crowd was a odd mixture of leftist factory workers, students and star-struck supporters of Poe and Joseph Estrada, a movie star friend of Poe who was ousted from the presidency amid a corruption scandal in 2001.
A sudden stampede interrupted the rally when a van opened its doors, revealing a large supply of bread offered as snacks. Afterwards, small groups of protesters began drifting away.
- with Philippine Star News Service, AFP