Pedro Ayala, a drug trafficker known to punish disloyal street dealers by pouring boiling water down their throats, had a reach that awed FBI agents. Here was a kingpin who could dial a number from Brooklyn Park and reach a Mexican cartel lieutenant in three rings of his cellphone.

After months of surveillance and wiretaps, federal agents had unraveled a spider web by which the cartel La Familia smuggled millions of dollars worth of methamphetamine from Mexico to Minnesota, then through Ayala and a St. Paul gang called Menace of Destruction. To them, it was the perfect case for prosecution by U.S. Attorney B. Todd Jones in Minneapolis.

But when FBI agents approached Jones’ office in early 2012 for funding to widen the investigation, they say, they were told it wasn’t developed enough. After several heated arguments, Jones’ office declined to take the case, and it wound up across the street in Hennepin County District Court — where drug sentences are generally less harsh and criminal conspiracies can be harder to prosecute.

The Ayala case, and others like it, help explain why a number of federal agents, judges and even prosecutors within Jones’ office have broken ranks over the past year with the man nominated by President Obama to run the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives (ATF). Last month, Donald Oswald, a former director of the FBI’s Minneapolis office, gave voice to their concerns in a letter to the U.S. Senate Judiciary Committee, calling Jones unfit to lead the federal agency.

In interviews with the Star Tribune over recent months, more than a dozen agents, judges and prosecutors elaborated on their concerns — detailing major drug and gang cases that Jones’ office refused to prosecute and describing an erosion of trust between the top law enforcement official in Minnesota and those assigned to tackle the government’s most dangerous cases. A federal judge has gone so far as to say that Jones’ office “compromised the judicial system” in one major gang case and put a federal prosecutor at risk.

While it’s not uncommon for law enforcement agents and prosecutors to feud over priorities, these tensions could surface as a theme at Jones’ Senate confirmation hearing this spring. Oswald and top federal agents in Minnesota are expected to be subpoenaed.

Jeanne Cooney, a spokeswoman for the U.S. attorney, acknowledged the frictions but said Jones has respected supporters as well. Thomas Heffelfinger, a previous U.S. attorney in Minnesota, and Michael Campion, former head of the Minnesota Bureau of Criminal Apprehension, have written letters on his behalf.

“With limited resources, Todd strategically chose to collaborate more intensely with county prosecutors,” Campion wrote. “They would tackle more narcotics cases, freeing up [his staff] to prosecute the most violent of violent offenders. I can’t argue with those priorities.”

At the same time, Jones has said his decisions reflect a larger shift in federal priorities — away from street crime and toward major conspiracies and white-collar fraud. In a memo last July to the U.S. Department of Justice, Jones wrote: “Over the last three years, this District has pivoted its focus in combating violent crime and narcotics, from numerous low-impact cases to organizational drug conspiracies and high threat offenders.”

To some federal agents, however, the scope of the Ayala case met Jones’ new standards perfectly, and its outcome only underscored their frustrations.

“You don’t get to an organized crime leader right off the bat,” Oswald said in an interview last year. “You start with some of the soldiers and you work the cases up. [But] they did not want to provide that sort of support.”

Jones has declined to comment on the Oswald letter, citing his pending Senate hearing.

Meth busts

In the past two years, Jones’ staff has turned away nearly 10 significant drug, gang and gun cases brought forward by the FBI and the Drug Enforcement Administration, according to court records, correspondence and interviews with agents. Some wound up being charged at the county level, where prosecutors have fewer tools to try complex cases, and several others eventually withered for lack of funding for wiretaps and surveillance. Records show that since Jones took office for his second term in 2009, indictments in major organized drug cases have declined by 50 percent, from 179 to 92.

In several cases reviewed by the Star Tribune, Jones’ office argued that agents submitted incomplete reports, made false claims to get wiretap funding, or refused to cooperate with prosecutors. For example, a senior manager claimed that FBI agents deliberately “undersold” the Ayala case in order to take it to Hennepin County — an “in-your-face” gesture designed to embarrass Jones.

Court documents and other records show that many of the cases did, however, involve multistate conspiracies with multiple defendants — the charging standard set by Jones.

In a case now being tried in Dakota County, for example, DEA agents have made 23 arrests and recovered more than 50 pounds of methamphetamine smuggled across state lines.

In a similar case in Ramsey County last year, DEA agents arrested 18 people and confiscated nearly 12 pounds of meth, a pound of cocaine and 30 pounds of marijuana. Federal agents identified cartel operatives who were later convicted in a St. Paul murder, and officers working the case came under gunfire from drug couriers just off Interstate 94 in St. Paul last year. Guilty pleas have been entered by many of the defendants.

Cooney says Jones’ office has tackled plenty of complex cases despite limited resources. One example is the Native Mob case now on trial in Minneapolis, where 24 defendants were indicted for drug dealing and more than 200 witnesses are expected to testify about a violence spree that has terrified Indian families statewide.

Frustrated judges

In addition to federal investigators, two Minnesota judges have also challenged Jones’ priorities. During a sentencing hearing in 2010, U.S. District Judge Donovan Frank said Jones’ office compromised “the interests of justice” by making and then breaking a plea agreement with a gang member who testified before a grand jury in return for a lighter sentence. Frank said the action put “the line prosecutor in harm’s way,” according to a court transcript, and “[damaged] the justice system.”

Cooney declined to discuss specifics of that case but said: “Prosecutors have their jobs and judges have their jobs, and sometimes they’re at odds with each other.”

A second jurist, Scott County Judge Rex Stacy, said he will no longer hear heroin cases investigated by federal task forces because Jones’ office hasn’t supported concerted pursuit of interstate heroin wholesalers. “We had the impression that the U.S. attorney was interested in cases that had large amounts of hard drugs, gangs and weapons. We were wrong,” Stacy said.

“Mexican cartels are pumping high-grade heroin to establish a customer base with the kids,” added Stacy, whose own daughter died of a heroin overdose several years ago. “Unless you prosecute these conspiracy cases federally, this is how you get a turf war with heads winding up in Dumpsters.”

Cooney said federal attorneys believed the defendants before Stacy were not significant enough under Jones’ policy and that some were already in jail. She also said Jones’ staff actually prevented the deportation of one dealer after Stacy argued that he should face prison time in the United States.

At a meeting last spring, tensions between Jones and top federal agents came to a boil. Two people in attendance, who spoke on condition of anonymity because they fear they risk losing their jobs, say Jones would not be second-guessed about the Ayala case and others. They say he pounded his fist on the table and told them that if they didn’t like his decisions, they could take the case “across the street” — to Hennepin County prosecutors.

The FBI did just that, and last fall Ayala was convicted of drug trafficking conspiracy.

Last December, Ayala found himself standing before a county judge for sentencing. She said she was treating him as if he’d been convicted in federal court, and not under state guidelines that might give him seven years. Ayala received 30 years in prison — the longest drug sentence in state history.