Hundreds of students and teachers have smashed windows and started fires inside a state capital building in southern Mexico, as fury erupted over the disappearance of 43 young people believed to have been abducted by local police linked to a drug cartel.

The protesters called for the safe return of the students from a rural teachers’ college in Guerrero state, who have been missing since 26 September. But fears are growing that their bodies may be in 10 newly discovered mass graves.

Associated Press photographs showed smoke billowing from the government building in Guerrero’s capital, Chilpancingo, and flames licking from office windows. Firefighters battled the blaze.

A spokesman for the Guerrero government said the protesters from a teachers’ union initially tried to get into the state congress in Chilpancingo but were repelled by anti-riot police. They then headed to the state government palace.

With the support of hundreds of students from the Ayotzinapa teachers’ college, the teachers blockaded the capital building, attacking it with iron bars, rocks and Molotov cocktails, he said.

The violence came more than two weeks after police in Iguala, also in Guerrero state, opened fire on teachers’ college students, killing at least six. Witnesses have said that dozens of students were taken away by police and have not been seen since. Twenty-six local police officers have been detained, and officials are trying to determine whether any of the students are in the mass graves nearby.

The confrontation in Iguala shed light on a widespread problem with local police in Mexico: they are often linked to organised crime. In the case of Iguala, the police who attacked the students were allegedly working with the local cartel, Guerreros Unidos, according to the testimony of those arrested.

Monday’s protests came as police in Guerrero shot and wounded a German university student in a reported case of mistaken identity, prosecutors said.

The victim, Kim Fritz Kaiser, was an exchange student at the Monterrey Institute of Technology, Mexico City campus, said the institute’s director, Pedro Grassa.

He told the Milenio TV station on Monday that Kaiser was in good condition and that the injury was not grave, though Kaiser would remain under observation.

Kaiser was in a van with other students – another German, two French and six Mexicans –travelling back from Acapulco and passing through Chilpancingo just after a confrontation between police and kidnappers that killed one officer.

Police tried to stop the van, believing it was suspicious. Police said they opened fire when they heard something that sounded like a shot or detonation, said Victor Leon Maldonado of the Guerrero state prosecutor’s office. The students kept driving, fearing that armed men might be trying to kidnap them, the state prosecutor, Inaky Blanco, said.

Maldonado told reporters in a press conference that the officers shot at the bottom of the van, trying to hit the tyres to make it stop. Kaiser was shot in the buttocks. The police involved have been detained and their weapons are being tested, according to a statement from the state attorney general’s office.

A US state department travel warning issued last week said American citizens should avoid Chilpancingo along with all parts of Guerrero state outside of the Pacific resorts of Acapulco, Ixtapa and Zihuatanejo and the tourist attractions of Taxco and the Cacahuamilpa caves.

A previous warning in January already advised against travel in the north-western part of the state near the border with Mexico state, where Iguala is located.