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.