FBI agents have looked into allegations of pay-for-play at the Clinton Foundation for more than a year despite the objections of Justice Department officials.
The foundation probe pitted FBI investigators against the Justice Department's top brass, who wanted to limit the bureau's law enforcement authority in the case, the Wall Street Journal reported Sunday evening.
The news comes as Hillary Clinton fends off fresh allegations of misconduct on the heels of a letter to Congress Friday from FBI Director James Comey indicating that agents had stumbled upon previously undisclosed emails related to their earlier investigation of Clinton's team and her private email server.
Democrats lashed out at Comey over the weekend, accusing the FBI director of taking unprecedented steps to malign Clinton just days ahead of the presidential election.
Sen. Harry Reid claimed Comey demonstrated a "double standard" by announcing the existence of a Clinton-related inquiry while covering up what could be "explosive" information about Donald Trump's alleged ties to Russia.
But the resurrected investigation into Clinton's activities goes far deeper than the "innuendo" Reid cited in his open letter on Sunday.
Four FBI field offices had joined the nationwide effort to collect evidence related to the Clinton Foundation earlier this year, the Journal reported.
However, Justice Department officials discouraged the effort during a meeting with agents in February. The FBI was told not to pursue additional law enforcement moves, such as witness interviews or subpoenas.
Some agents reportedly kept at the probe using the methods already approved by the Justice Department. In August, a senior Justice Department official called Andrew McCabe, deputy director of the FBI, to say the department was worried that the FBI continued to investigate the Clinton Foundation despite the agency's push to end that inquiry.
While some agents reportedly said they were authorized to continue their investigation, others said McCabe issued a stand-down order after the Justice Department official's call.
FBI agents were blocked from accessing emails uncovered during a separate investigation into Clinton's treatment of classified material due to the immunity agreements provided to aides who handed over the records.
The Clinton Foundation-related details were just the latest to suggest Clinton's legal troubles are far from finished.
While Clinton and her allies have spent months touting the FBI's closure of the email probe as proof that she did nothing wrong, Comey's letter indicated she and her aides could still face consequences for their conduct while she served as secretary of state.
The emails that triggered Comey's renewed interest in the Clinton probe were discovered on at least one laptop belonging to Huma Abedin, Clinton's former deputy chief of staff, and Anthony Weiner, her estranged husband.
FBI agents seized the devices during a separate investigation into whether Weiner sent sexually-charged messages to an underage girl.