If it holds that lead, that would see the PRI make a comeback as the leading force in the 500-seat lower house, although it remains to be seen whether the party will win an outright majority.
Earlier, exit polls conducted by national media had put the PAN about 11 points behind the PRI which ruled Mexico for 71 years before losing the presidency in 2000.
The vote is the first real test of Calderon's popularity since the disputed 2006 election that brought him to office.
If the PRI gains the upper hand in congress, it is likely to frustrate Calderon's reform plans to heal Mexico's recession-hit economy.
Calderon wants to overhaul Mexico's energy sector to allow more private investment in the search for oil in the Gulf of Mexico, as well as reform the country's tax system and labour laws.
But if Sunday's results hold, he will have to negotiate with the centrist PRI to push reforms through congress.
The PRI has already watered down earlier reform attempts by Calderon, who has not had a majority in congress since he became president.