Supporters of the opposition Party of the Democratic Revolution (PDR) threw rocks at police who were attempting to break up their blockade of the country's parliament in Mexico City on Monday.
Police responded with baton charges and tear gas. Eight demonstrators were injured.
The protestors have been demanding a full recount of the July 2 election which was narrowly won by Felipe Calderon of the ruling National Action party.
The country's electoral court has said that a full recount would be illegal and instead held a partial recount of 9% of ballot boxes.
The partial recount was completed on Sunday but the results have not yet been formally announced.
The trouble began on Monday when police attempted to break up a large demonstration in front of the country's parliament.
Demonstrators then threw rocks at the federal police lines.
It was the first time the government has deployed police to break up protests that began days after the election and have until now been peaceful.
"They hit us all, they fired gas at us. I still haven't recovered from the tear gas," Elias Moreno, a PDR senator, said.
Supporters of Andres Manuel Lopez Obrador, the PDR leader, who claims the election was stolen by Calderon, have turned the centre of Mexico City into a sea of tents and extended their protests to the country's parliament on Monday.
Huge protests have given way to a war of attrition
Dozens of protesters have put up tents on one side of the imposing concrete building.
They want to stop Vicente Fox, Mexico's outgoing president, from delivering his annual state of the nation speech there on September 1.
Calderon, the candidate of Fox's National Action party, said on Monday a partial vote recount carried out last week has confirmed his victory.
He is confident Mexico's top electoral court will now declare him president-elect, he said.
Breaking several days of silence in the bitter fight over the election result, Calderon said no serious irregularities were found in the recounted ballot boxes.
"Not one significant anomaly was found," Calderon said. "On the contrary, it ratifies ... that we won the elections."
The electoral court has begun studying the recount results to see if there was any evidence of the massive fraud alleged by Lopez Obrador, the former mayor of Mexico City, who promises to end free-market reforms and pull millions out of poverty.
The court must formally declare a winner by September 6 but Calderon said he hopes his victory will be officially confirmed before then.
Lopez Obrador says the recount, called by the court at the request of the PDR, showed tens of thousands of votes were miscounted or are simply missing from polling stations.
On Monday, his supporters also blockaded several office buildings of Banamex, a bank group owned by US-based Citigroup, and stopped employees from going to work.
Lopez Obrador wants all 41 million votes counted again and warns he will extend a campaign of civil resistance if the court rules in Calderon's favour.
"The confrontation, the post-electoral crisis, is going to get worse," said PDR spokesman Gerardo Fernandez.
Calderon insisted a total recount was unnecessary. The official result from the July election gave him a winning margin of about 244,000 votes, or 0.58 of a percentage point.
Last week, supporters of Lopez Obrador briefly blocked access to the stock exchange, foreign-owned banks and the finance ministry.
Mexico City's police have largely avoided confrontation with the demonstrators in the PDR-administered capital.