The revelation comes as President Donald Trump and congressional Republicans have been urging the Justice Department to look into corruption allegations involving the foundation.
What will inquiry focus on?
The FBI and the Department of Justice have not delivered an official statement regarding an active investigation.
The Justice Department has opened up an new investigation into the Clinton Foundation to see if it conducted "pay-to-play" politics or other illegal activities while Hillary Clinton was secretary of state, The Hill reported on Thursday.
The FBI has been quietly investigating the Clinton Foundation for months, according to people familiar with the inquiry, United States media report. In November, the Justice Department wrote that Sessions would direct senior prosecutors to look into the cases about which they raised concerns and hinted that some might already be under investigation. The inquiry ultimately ended without criminal charges.
Some reports have linked contributions and speech fees relating to the charity with decisions by Clinton's State Department that benefited donors.More news: Twins born in different years as first New Year's babies arrive
During the campaign, Trump supporter Jeff Sessions, then an Alabama senator and now the attorney general, suggested that Clinton used her high position as secretary of state to "extort" global governments for her family's foundation.
Mr Clinton remains the foundation's president, and the couple's daughter, Chelsea, sits as vice-chair. In 2016, Justice Department prosecutors rejected a request from FBI agents to expand and intensify the foundation investigation, these people said.
"The fundamental thing is you cannot be secretary of state of the United States of America and use that position to extort or seek contributions to your private foundation", he told CNN's Alisyn Camerota on "New Day" in 2016.
Foundation spokesman Craig Minassian told The Hill that "time after time, the Clinton Foundation has been subjected to politically motivated allegations, and time after time these allegations have been proven false".
Clinton's chief spokesman, Nick Merrill, on Friday morning excoriated the Federal Bureau of Investigation for re-opening the case, calling the probe "disgraceful" and suggesting it was nothing more than a political distraction from President Trump's Russian Federation controversies. The goal is to distract from the indictments, guilty pleas, and accusations of treason from Trump's own people at the expense of our justice system's integrity.