The ruling National Action party, or PAN, led by Felipe Calderon, Mexico's president, lost to the PRI in two central states, indicating that the poor state of the economy and unrelenting violence linked to drug gangs was hurting the central government.
Calderon's allies, however, did make some surprise victories. Exit polls predicted wins for PAN in three southern states, which for decades were strongholds of the PRI, thereby nullifying the opposition group's gains.
Eyeing 2012 polls
With Mexico's left divided and Calderon sinking in opinion polls, the PRI is eyeing a return to national power in 2012, two terms after PAN ended its 71-year rule in 2000.
Al Jazeera's Franc Contreras, reporting from Mexico City, said people were already talking about the possibility of a 2012 election victory.
"Last year in mid-term elections the PRI took control of the lower house of congress once again," he said.
"Mexicans have not had faith in the right-leaning party that is currently in power here, and they are talking about the devil they know returning to power."
Campaigning in the run-up to Sunday's polls was blighted by drug gang intimidation in northern states as suspected cartel hitmen murdered two candidates and threatened others in recent weeks.
It was some of the most blatant evidence of traffickers interfering in politics since Calderon came to power in late 2006 and launched a drug gang crackdown that has left more than 26,000 people dead, mostly from drug gangs and the police.
Only a few incidents of violence were reported throughout the course of Sunday's election.
In the city of Durango, armed men stole ballot boxes from a polling station, while in Ciudad Juarez, police were investigating the killing of a couple gunned down while walking home.
Turnout overall in towns around Ciudad Juarez, which feuding cartels have turned into one of the world's deadliest cities, was only around 20 per cent.
Al Jazeera's Mariana Sanchez, reporting from Cuidad Juarez, said there were mixed feelings regarding Sunday's election.
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"There was some voter apathy, but some also felt it was their duty to vote and believe change can be brought about.
"However, many here also do not trust politicians, considering the security situation has been so bad," she said.
"The governors in many parts of Mexico run their states like fiefdoms, but after this election, we may see them working closely with President Felipe Calderon in light of the deteriorating security situation and the fact that some drug cartels are gaining further ground.
"I think they now know they can no longer work autonomously."
In the northeastern state of Tamaulipas, which has been plagued by drug gang-related violence, long lines formed at polling stations during the day after around 40 per cent of election volunteers quit fearing attacks.