MEXICO CITY — In their joint fight against drug traffickers, the United States and Mexico have forged an unusually close relationship in recent years, with the Americans regularly conducting polygraph tests on elite Mexican security officials to root out anyone who had been corrupted.But shortly after Mexico’s new president, Enrique Peña Nieto, took office in December, American agents got a clear message that the dynamics, with Washington holding the clear upper hand, were about to change.“So do we get to polygraph you?” one incoming Mexican official asked his American counterparts, alarming United States security officials who consider the vetting of the Mexicans central to tracking down drug kingpins. The Mexican government briefly stopped its vetted officials from cooperating in sensitive investigations. The Americans are waiting to see if Mexico allows polygraphs when assigning new members to units, a senior Obama administration official said.In another clash, American security officials were recently asked to leave an important intelligence center in Monterrey, where they had worked side by side with an array of Mexican military and police commanders collecting and analyzing tips and intelligence on drug gangs. The Mexicans, scoffing at the notion of Americans’ having so much contact with different agencies, questioned the value of the center and made clear that they would put tighter reins on the sharing of drug intelligence.There have long been political sensitivities in Mexico over allowing too much American involvement. But the recent policy changes have rattled American officials used to far fewer restrictions than they have faced in years.Asked about security cooperation with Mexico at a news conference on Tuesday, President Obama said: “We’ve made great strides in the coordination and cooperation between our two governments over the last several years. But my suspicion is, is that things can be improved.”Mr. Obama suggested that many of Mexico’s changes “had to do with refinements and improvements in terms of how Mexican authorities work with each other, how they coordinate more effectively, and it has less to do with how they’re dealing with us, per se.” He added, “So I’m not going to yet judge how this will alter the relationship between the United States and Mexico until I’ve heard directly from them to see what exactly are they trying to accomplish.”Mr. Obama is scheduled to visit Mexico on Thursday and Friday on a mission publicly intended to broaden economic ties.But behind the scenes, the Americans are coming to grips with a scaling back of the level of coordination that existed during the presidency of Felipe Calderón, which included American drones flying deep into Mexican territory and American spy technology helping to track high-level suspects.In an interview, Mexico’s interior minister, Miguel Ángel Osorio Chong, made no apologies. He defended the moves, including the creation of a “one-stop window” in his department to screen and handle all intelligence, in the name of efficiency and “a new phase” in fighting crime.In a country worn down by tens of thousands of people killed in a drug war, he said Mexico needed to emphasize smart intelligence over the militarized “combating violence with more violence” approach of the Calderón years.But American officials here see the changes as a way to minimize American involvement and manage the image of the violence, rather than confronting it with clear strategies.The lack of certainty over Mexico’s plans and commitment has jeopardized new security assistance from the United States. Plans to release $246 million, the latest installment of a $1.9 billion anticrime package known as the Merida initiative, have been held up by Senator Patrick J. Leahy, Democrat of Vermont. His office has been waiting for months for more details from the State Department and the Mexican government on how the money would be spent and what it might accomplish.A senior administration official, speaking on the condition of anonymity to provide a more candid assessment, said a recent visit by Mr. Osorio Chong to Washington helped calm some fears. A delegation of Mexican officials is also expected to visit in the coming weeks to explain the country’s plans to members of Congress.But there is growing anxiety that the violence has not diminished, with daily killings hovering around 50 since last fall. Some American officials say they are increasingly worried by public and private signs suggesting that Mr. Peña Nieto, the young face of the Institutional Revolutionary Party, which ran Mexico for 71 years, is putting the government’s crime-fighting image above its actions.“The cosmetics — that’s what they care about,” one American official said, insisting on anonymity so as not to worsen already tense relations.“The impression they seem to want to send is ‘We got this,’ ” one former American official said, asking for anonymity because he was discussing private conversations. “But it’s clear to us, no, they don’t. Not yet.”A senior administration official, asked for a sign of progress or a recent accomplishment in security matters, struggled with the question until pointing to the extradition to the United States of a few men on drug charges, conceding they were not big fish. Other extradition requests appear stalled; there were 155 last year, mostly for drug offenses, the highest in nearly a decade.Tuesday evening, less than 48 hours before Mr. Obama’s arrival and with mounting questions on whether Mexico would go after kingpins, Mexico announced it had captured Inés Coronel, the father-in-law of the most-wanted capo, Joaquín Guzmán Loera, known as El Chapo. It was unclear if the United States played a role in the arrest.If so, it would represent a step beyond the Mexican discomfort with Americans operating on their turf that emerged in December, just after Mr. Peña Nieto’s inauguration. It solidified after an explosion on Jan. 31 at the office complex of the state oil company, Pemex, in which 37 people died and more than 120 were injured.Agents with the Bureau of Alcohol, Tobacco, Firearms and Explosives were invited to help investigate. But after they suggested in a preliminary assessment that a bomb might have caused the blast, the agency’s role in the investigation was cut short, American officials said, adding that Mexican officials canceled a visit by a team of investigators from the United States.An administration official said that while American explosives experts were not allowed to contribute as much as they could have to the investigation, creating a sense that the Mexicans were rushing to conclude that the blast was an accident.On Feb. 4, the attorney general of Mexico announced that the cause was an unexplained buildup of gas, possibly methane, that was ignited by a spark in the basement of one of the buildings.The American ambassador was invited to the news conference on the findings, but a State Department official said the level of American involvement in the investigation did not warrant the ambassador’s presence. With the American agents leaving the cooperative center in Monterrey, which was first reported by The Washington Post on Sunday, and the development of the one-stop intelligence mechanism, the United States is worried and is seeking more information.“We’re still figuring out what that means,” a senior administration official said of the new intelligence arrangement.But the fear is that it will diminish the access that American law enforcement and intelligence agencies have established with branches of the Mexican police and military. Those hard-fought relationships could disintegrate if American agents have to go through a central office to communicate and share knowledge with their Mexican counterparts, some American officials say.Randal C. Archibold and Damien Cave reported from Mexico City, and Ginger Thompson from New York.