The statement undermines a report from a team of CNN reporters in August that the Justice Department quashed an investigation into the Clinton family’s non-profit earlier this year, The Daily Caller is reporting.
“The FBI has an intensive investigation ongoing into the Clinton Foundation,” Fuentes said Saturday, citing current and former senior FBI officials as sources.
“The reports that three divisions came in with a request to Washington to open cases and that they were turned down by the Department of Justice, that’s not true,” he said, referring to the CNN report.
“What was turned down was that they be the originating office. Headquarters at the FBI made the determination that the investigation would go forward as a comprehensive unified case and be coordinated,” he added.
According to the CNN report, officials with the FBI and Justice Department met in Washington earlier this year to discuss opening an investigation into possible conflicts of interest between the Clinton Foundation and Hillary Clinton State Department.
Several FBI field offices and U.S. attorneys offices pushed for the investigation after receiving a tip from a bank about suspicious donations to the Clinton Foundation from a foreign donor, according to the report.
The Justice Department prevailed in that standoff and nixed the investigation, CNN reported.
Fuentes was discussing the investigation in the context of a letter that FBI director James Comey sent to Congress on Friday stating that the bureau was reopening the investigation into Clinton’s emails.
“In connection with an unrelated case, the FBI has learned of the existence of emails that appear pertinent to the investigation,” Comey wrote.
“I am writing to inform you that the investigative team briefed me on this yesterday, and I agreed that the FBI should take appropriate investigative steps designed to allow investigators to review these emails to determine whether they contain classified information, as well as to assess their importance to our investigation.”
The emails were reportedly recovered from a laptop shared by Clinton aide Huma Abedin and her husband, disgraced former congressman Anthony Weiner.
The FBI, Justice Department and New York state’s attorney are all investigating Weiner over text messages he sent to a 15-year-old girl from North Carolina. Several outlets reported that Clinton did not send or receive the newly-recovered emails, which reportedly number in the thousands.
Clinton criticized Comey during a campaign speech, calling his letter to Congress “unprecedented” and “deeply troubling.”
Fuentes asserted that the emails could pertain to the original Clinton email investigation, which was closed in July, as well as to the Clinton Foundation probe.
“In a sense, it’s almost turned into a one-stop shopping for the FBI as they could have implications affecting three separate investigations on one computer,” said Fuentes, who served as assistant director at the FBI during the George W. Bush administration.
In August, The Daily Caller News Foundation’s Richard Pollock reported that Preet Bharara, the U.S. attorney for Southern District of New York, was investigating the Clinton Foundation in coordination with the FBI.