Security guards said about 300 people pushed through the gates of the compound of the Department of Agriculture, in a northern suburb of Manila, unfurling banners reading: "Ensure the welfare of rural workers."
Police escorted dozens of protesters from left-wing farmers' groups from the main building, while witnesses said the protesters broke windows, attacked guards with sticks and chanted: "End the Gloria regime."
"They have peacefully dispersed," police Superintendent Raul Petrasanta said, adding that an official talked to Friday's protesters and set a date for a formal meeting.
One worker inside the building, Secretary Domingo Panganiban, said: "We've locked our doors."
Panganiban had been sworn in to his post earlier on Friday at the presidential palace.
A doctor at the farm department's clinic said three people were injured, including a security guard and a protester.
A collection of rural groups said in a statement they went to the agriculture department to criticise policies that were hurting Filipino farmers with cheaper imports and to demand Arroyo make good on promises of jobs, loans and land development.
About 30,000 protesters had gathered peacefully in Manila on Wednesday, calling for Arroyo to step down over allegations of election fraud and graft involving her family.
The president has refused to resign and has been rebuilding her cabinet and base of allies after resignations and defections last week.
Filipino protesters want
President Arroyo to step down
Weeks of uncertainty have kept investors nervous and raised fears that a protracted political battle will paralyse Arroyo's reforms aimed at raising revenues and cutting debt.
But there is no sign the middle class, whose participation was crucial to so-called people-power revolts that toppled presidents in 1986 and 2001, has joined the rallies by Arroyo's political enemies and groups of leftists, students and farmers.
Lift in markets
Philippine financial markets were lifted on Friday by expectations the Supreme Court will end its freeze on a tax expansion at the heart of the government's fiscal reform plans.
Markets also got a boost from news the government posted a monthly budget surplus in June, its second this year, which raised hopes that fiscal improvement could continue despite the political crisis.
The court has said it would issue a final ruling on whether the expanded sales tax was constitutional within the month.
The justices said late on Thursday the government and its challengers, petroleum dealers and opposition parties, had to submit a summary of their arguments by 24 July.