Last May, a team of federal agents chasing the sons of Joaquín Guzmán Loera, the Mexican drug lord known as El Chapo, caught a break.

Through a combination of electronic data and human intelligence, the agents had tracked one of the sons — Jesús Alfredo Guzmán Salazar — to a location in the western Mexican state of Sinaloa.

Eager to jump into action, the team prepared to work with the Mexican military and go after Mr. Guzmán Salazar, one of the world’s most wanted criminals.

But in the end, according to records obtained by The New York Times and three people familiar with the matter, they were told to stand down by the Justice Department. Another federal agency, the Drug Enforcement Administration, was separately investigating Mr. Guzmán’s sons and it was thought that any active measures to take them into custody could disrupt that inquiry — or even get people killed.

Under the best circumstances, it is challenging for U.S. federal agents to chase drug lords in Mexico, where they are required to work with local partners who can often be unreliable or untrustworthy. But the episode involving Mr. Guzmán Salazar — one of four sons of El Chapo who are known as the Chapitos — points to a problem closer to home: the rivalries that can erupt when different law enforcement agencies go after the same targets.

The quarrel in this case pitted officials at the D.E.A., who helped bring a sprawling indictment against the Chapitos in New York, against federal prosecutors and agents in Chicago, Washington and San Diego, who joined forces to bring their own case against Mr. Guzmán’s sons.

Neither the dispute nor its consequences were visible last month when Attorney General Merrick B. Garland — flanked by representatives from all of the agencies — gathered in Washington to announce the new indictments against the Chapitos. Mr. Garland celebrated the collective charges as a sweeping assault against the ability of the Guzmáns’ organization, the Sinaloa drug cartel, to ship fentanyl and other drugs from Mexico across the U.S. border.

“The Justice Department is attacking every aspect of the cartel’s operations,” Mr. Garland said.

This week, taking note of the behind-the-scenes spat, Senator Charles E. Grassley, Republican of Iowa, sent a letter to Mr. Garland and to the heads of three federal law enforcement agencies, asking for an explanation about how the pursuit of the New York case in particular may have “impacted any attempts to arrest or capture” Mr. Guzmán’s sons.

The letter also requested any records related to how the D.E.A., the F.B.I., several U.S. attorney’s offices and Homeland Security Investigation, the investigative section of the Department of Homeland Security, had “de-conflicted” the various cases concerning the Chapitos.

The roots of the squabble reach back to the fall of 2021, when senior leaders at the D.E.A. learned that agents in one of their top investigations units — known as the 959 Group — had covert sources who claimed they had insight into the Chapitos’ bustling fentanyl business, according to a senior D.E.A. official.

Fentanyl, which kills tens of thousands of Americans a year, was a top priority for Anne Milgram, the administrator of the D.E.A., who vowed after taking control of the agency to bring down the cartels most responsible for selling it.

The senior official said the D.E.A. immediately saw the possibility of building a major case that could attack not just the Chapitos themselves, but their entire fentanyl network: chemical producers, money launderers, smugglers and distributors. The plan, the official added, was to bring together everything the D.E.A. knew about the Chapitos to bolster the 959 Group’s inquiry, which was being conducted with the U.S. attorney’s office in Manhattan.

Around the same time, federal prosecutors in Chicago, San Diego and Washington — some of whom had been investigating the Chapitos for the better part of a decade — came up with a different plan. They wanted to merge three separate cases they had been working on involving Mr. Guzmán’s sons into a single case based in Chicago, according to five people familiar with the matter.

The Chicago case did not focus directly on the Chapitos’ fentanyl operation, but it took a sweeping look at the men’s drug sales and violent crimes reaching back, in some instances, to 2008. It was built on the work of a coalition of agents from the D.E.A., the F.B.I. and Homeland Security Investigations and incorporated a vast trove of evidence from a stable of cooperating witnesses and an initial round of indictments against the Chapitos.

Jesús Alfredo, for example, had first been charged in Chicago in 2015 and his brother, Iván Archivaldo Guzmán Salazar, had first been charged in San Diego one year earlier. Prosecutors in Washington had unsealed charges against their two half brothers — Ovidio Guzmán López and Joaquín Guzmán López — in 2019, just days after the father was convicted on all charges at his own trial in Federal District Court in Brooklyn.

The two sides — those involved in the Manhattan case and those involved in the Chicago case — disagree on what happened next.

Five people associated with the Chicago prosecution claim that the D.E.A. pulled its resources out of their broader investigation just as it was reaching completion in favor of the New York fentanyl case. The senior D.E.A. official said the agents working on the Chicago case were simply told to put their involvement in it on hold until the conflict was resolved through a kind of mediation process.

In the end, the senior D.E.A. official said, officials at the Justice Department, serving as arbiters, secured an agreement about how to proceed. The consolidated Chicago case could move forward, the D.E.A. official said, provided that the prosecutors in charge of it coordinated with their New York counterparts and did not take any “proactive” measures that might expose the sources working with the 959 Group or otherwise harm the New York prosecution.

But some people associated with the Chicago case saw things differently. They believed the Justice Department had effectively ordered them to stand down on bringing their updated indictment until the prosecutors in New York had a chance to catch up and finish their work.

Fights among competing law-enforcement agencies are, of course, routine in high-profile criminal cases. Over the years, multiple law-enforcement agencies — from New York to Nogales, Ariz. — took part in the hunt for the elder Mr. Guzmán, leading to his final arrest in 2016 and his extradition to the United States in 2017.

By the time El Chapo went to trial in Brooklyn, he was already facing indictment in six other cities. He was convicted in early 2019, largely based on accounts from several former aides who testified against him and on sophisticated wiretaps of his communications system.

But both sides seem to agree that the dispute over the dueling Chapitos cases was more painful and contentious than usual.

Indeed, the Justice Department stepped in again last spring as the F.B.I. and Homeland Security Investigations homed in on some of the men. There were already provisional arrest warrants in Mexico for all four Chapitos based on the pre-existing indictments, and several people involved in the consolidated case said that when the possibility of an arrest arose in May 2022, they wanted to take it.

But when word reached the D.E.A., the agency sent up an alarm, the senior D.E.A. official said. Any attempt to go after the Chapitos at that point would have risked the life of at least one of the 959 Group’s sensitive sources, the official said.

The D.E.A. official also noted that the agency never sought to stop the Mexican authorities from taking down the Chapitos on their own. And in January they did just that: Mexican security forces arrested Ovidio Guzmán López.

The capture came after the Mexican authorities had briefly detained Mr. Guzmán López and then released him in October 2019 as cartel gunmen unleashed a wave of gun attacks, burned cars and took members of the security forces hostage.

It remains unclear when Mr. Guzmán López might be extradited to the United States and, if he ultimately is, whether he will stand trial on the New York fentanyl charges or on one of the other indictments. His brothers remain at large in Mexico.

Complicating matters, the flurry of activity involving the Chapitos has come at a moment of a profound tension between U.S. and Mexican officials over their deteriorating law-enforcement relationship — and in particular, the issue of who is to blame for the scourge of fentanyl.

In February, Ms. Milgram lashed out at the Mexican government, saying officials there had offered no assistance to U.S. agents working on cases involving fentanyl from Mexico. Weeks later, President Andrés Manuel López Obrador shot back with baseless claims that his country had nothing to do with the drug.

Even the Chapitos themselves have waded into the fray.

This month, they released a letter to the Mexican news media, denying the U.S. government’s claims that they deal in fentanyl at all.

“We have never produced, manufactured or marketed fentanyl or any of its derivatives,” the letter said. “We are victims of persecution and they made us a scapegoat.”