Mexicans are heading to the polls for midterm elections despite violent protests in parts of the country.

Protesters burned ballot boxes in several states of southern Mexico in an attempt to disrupt Sunday's elections seen as a litmus test for President Enrique Pena Nieto's government.

Thousands of soldiers and federal police were guarding polling stations where violence and calls for boycotts threatened to mar elections for 500 seats in the lower house of Congress, nine of 31 governorships and hundreds of mayors and local officials.

Election authorities said 99 percent of polling stations remained open despite the violence.

After casting his ballot in Mexico City, Pena Nieto said there were only reports of "isolated incidents" and that it was "rather satisfying to know that the great majority of polling stations were installed".

Midterm elections usually draw light turnout, but attention was unusually high this time as a loose coalition of radical teachers' unions and activists vowed to block the vote.

The teachers' demands include wage hikes, an end to teacher testing and the safe return of 43 students who disappeared last September. Prosecutors say they were killed and incinerated by a drug gang.

RELATED: Demanding the return of 43 missing students

Protesters burned at least seven ballot boxes and election materials in Tixtla, the Guerrero state town where the teachers' college the missing students belonged to is located.

"We want the children to be found first, and then there can be elections," Martina de la Cruz, the mother of one of the missing students, told the AP news agency.

Soon after, there was an exchange of rock-throwing between protesters and hundreds of people who said they intended to defend their right to vote. There were no immediate reports of injuries.

Ballot boxes were also destroyed in the southern states of Chiapas and Oaxaca. In Oaxaca's capital, masked protesters emptied a vehicle of ballots, boxes and voting tables and burned the material in the main square.

Municipal policeman Onesimo Rojas said masked protesters torched ballot boxes in at least eight places in the city. The state government reported 88 arrests related to the destruction of election materials and disturbances in the capital, Tuxtepec and Salina Cruz.

Al Jazeera's Adam Raney, reporting from Mexico City as exit polls were released on Sunday night, said an independent candidate appeared to have won a "groundbreaking victory" in the vote for governor in the northern Nuevo Leon state.

Exit polls suggested that Jaime Rodriguez won 46 percent of the vote with his strongest challenger far behind at 29 percent.

"He's known as a rugged, maverick guy," our correspondent said. "He used to be a member of the ruling party, the PRI, but this year he launched an independent campaign, relying more on social media than on big funds to get his word out and won with about 46 percent of the vote."