Pena Nieto said Thursday that his government remains committed to fighting organized crime, but the United States and Mexico must "cooperate on the basis of mutual respect, to be more efficient in our security strategy that we are implementing in Mexico."
Obama stressed that the countries will continue to cooperate closely on security, but he didn't specify how.
"I agreed to continue our close cooperation on security, even as that nature of that close cooperation will evolve," he said.
It's up to the Mexican people, Obama said, "to determine their security structures and how it engages with other nations, including the United States."
High-profile cartel takedowns were a hallmark of former President Felipe Calderon's tenure. Pena Nieto has vowed to take a different approach, focusing more on education problems and social inequality that he says fuel drug violence. The details of his policies are still coming into focus, and analysts say his government has deliberately tried to shift drug violence out of the spotlight.
Before Obama's arrival, a spate of news reports this week on both sides of the border detailed changes in how Mexico cooperates with the United States.
Under the new rules, all U.S. requests for collaboration with Mexican agencies will flow through a single office, Interior Minister Miguel Angel Osorio Chong told Mexico's state-run Notimex news agency.
It is a drastic change from recent years, when U.S. agents enjoyed widespread access to their Mexican counterparts.
Critics have expressed concerns that Pena Nieto's government will turn a blind eye to cartels or negotiate with them -- something he repeatedly denied on the campaign trail last year. On Tuesday -- two days before Obama's arrival -- his government arrested the father-in-law of Joaquin "El Chapo" Guzman, head of Mexico's Sinaloa cartel and one of the country's most-wanted drug lords.
But with the focus on the economy, Pena Nieto said the presidents agreed to create a new high-level group to discuss economic and trade relations between the two nations. The group, which will include Cabinet ministers from both countries and Vice President Joe Biden, will have its first meeting this fall, the Mexican president said.
Imports and exports between the United States and Mexico totaled nearly $500 billion last year, and before Obama's arrival officials on both sides of the border said economic relations would be a focal point during the U.S. president's visit.
Later, he traveled to Costa Rica, where he met with President Laura Chinchilla and other regional leaders.
Obama pledged continued U.S. support to the Central American Regional Security Initiative, saying "with the absence of security," it is very hard to develop economically.
"Problems like narco-trafficking arise when a country is vulnerable because of poverty and institutions not working for people," he said.
"The stronger the economy and institutions for individuals seeking legitimate careers, the less powerful these narco-trafficking operations are going to be."