Riot police clashed with protesters in running street battles as black smoke billowed from the white two-story building of the Institutional Revolutionary Party (PRI) in the southern state's capital, Chilpancingo.
Some 1 000 people, including students and members of the radical CETEG teachers union, had marched in the city before battling police, throwing stones and firebombs.
At least five people were injured after being hit by rocks, including three officers and two journalists, a civil protection official told AFP. One of them is a photographer working for AFP.
"Some 400 people seized the PRI building and some workers, whom they later freed", the party's state president, Cuauhtemoc Salgado, told Milenio television.
The office had undergone renovations after it was torched last year by protesters angry at a controversial education reform.
Violent protests have erupted in Mexico since authorities said on Friday that gang hit men confessed to murdering the students and incinerating their bodies after corrupt police handed over the 43 young men in September.
The crime has undermined Pena Nieto's assurances that his security strategy was bearing fruit and reducing drug-fuelled violence that has killed more than 80 000 people since 2006.
The crime has also hurt his efforts to shift Mexico's narrative away from drug cartel mayhem and toward economic and political reforms that have won international acclaim.
Pena Nieto was in China for a summit on Tuesday despite criticism over his decision to travel in the midst of the crisis.
Protesters besieged the airport of Guerrero's Pacific resort of Acapulco for three hours on Monday, forcing three flight cancellations, after clashing with police.
On Saturday, a group of 20 demonstrators briefly set fire to the wooden door of the National Palace in Mexico City at the end of a march that had drawn thousands of people.
Law officials to meet families
Authorities say gang-linked police shot at busloads of students in the Guerrero city of Iguala on 26 September, in a night of violence that left six people dead.
The police then handed the 43 abducted students to the Guerreros Unidos drug gang, prosecutors say.
Authorities say Iguala's mayor ordered police to confront the students over fears they would interrupt a speech by his wife, who aspired to succeed him.
The students had travelled to Iguala to raise funds but hijacked four buses to return home, a common practice among the young men from the college known for its radical left-wing politics.
Officials stopped short of declaring the students dead, stressing they were waiting for DNA results.
Parents of the missing students, who deeply distrust the government, say they will only believe their sons are dead once they get independent DNA test results.
Interior minister Miguel Angel Osorio Chong and attorney general Jesus Murillo Karam were scheduled to meet with the families on Tuesday.
Pena Nieto was in Beijing for an Asia-Pacific Economic Co-operation (Apec) summit and a state visit.
After China, a country with which he has sought closer ties, Pena Nieto will travel to Brisbane, Australia, for the summit of the Group of 20 major economies. He comes home on Saturday.