However, the probe's very existence already has led to accusations from Democrats that the Republican administration is pursuing old, dead cases to punish political enemies. A continued probe of Clinton could be viewed, particularly by Republicans, as the department being evenhanded in its approach to political cases.
Ron Hosko, a former assistant FBI director, said the bureau has been thrust into a "political minefield," with pundits criticizing its every move.
"This is where big boys earn their pay, and this is where I think you put your nose to the grind stone," Hosko said.
The Justice Department declined to comment. The Clinton Foundation inquiry was first reported by The Hill.
In a statement, Clinton Foundation spokesman Craig Minassian said: "Time after time, the Clinton Foundation has been subjected to politically motivated allegations, and time after time these allegations have been proven false. None of this has made us waver in our mission to help people. The Clinton Foundation has demonstrably improved the lives of millions of people across America and around the world while earning top ratings from charity watchdog groups in the process. There are real issues in our society needing attention that the Clinton Foundation works hard to solve every day. So we're going to stay focused on what really matters."
The Clinton Foundation probe dates back to 2015, when FBI agents in Los Angeles, New York, Little Rock and Washington began looking at those who had made donations to the charity, based largely on news accounts, according to people familiar with the matter.
But in 2016, Justice Department prosecutors rejected a request from FBI agents to expand and intensify their work. They asked that the bureau not take any investigative steps that could become public, out of worry that could affect the impending election.
The investigation resumed some time after the election, with the FBI's Little Rock office taking the lead, said one person familiar with the matter. Still, there was some skepticism inside the Justice Department that it would ever produce charges.
"It was never a great case, but it's still being worked," one person familiar with the probe said.
Republicans in particular have long raised concerns about what they viewed as corruption and conflicts of interest at the Clinton Foundation, in particular Hillary Clinton's dealings with its donors while she was secretary of state. GOP lawmakers had called on Attorney General Jeff Sessions in July and again in September to explore various Clinton Foundation dealings, as well as other matters, by appointing a special counsel to look into Clinton-related issues. 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.
Assistant Attorney General Stephen Boyd wrote at the time that part of what the department would do was assess whether "any matters currently under investigation require further resources," although he said his letter should not be construed as confirming or denying any probe.
By that time, according to the people familiar with the matter, agents already were investigating the Clinton Foundation.
The foundation inquiry is separate from the FBI's high-profile investigation into Hillary Clinton's use of a private email server while she was secretary of state, although Republicans have said that probe, too, needs to be reopened. The email investigation focused on whether Clinton or her aides mishandled classified information by using the private server. The FBI's director at the time, James Comey, recommended in July 2016 the case be closed without charges, and although work on it briefly resumed in October - soon before the presidential election - he ultimately did not change his mind, and the Justice Department endorsed his recommendation.
Justice Department officials have said senior prosecutors also are reviewing investigative records on the Clinton email case to see if any of the concerns raised by Republican lawmakers merit appointment of a special counsel for further investigation.
Word of the ongoing foundation probe came shortly after Rep. Mark Meadows, R-N.C., and Rep. Jim Jordan, R-Ohio, suggested in a Washington Examiner column Thursday that it might be time for a new attorney general.
Trump has publicly toyed with removing Sessions, and he has repeatedly criticized the Justice Department and said his attorney general should look into Clinton and her allies, taking aim most recently at top Clinton aide Huma Abedin. On the campaign trail, Trump's supporters frequently chanted "Lock her up!" at the mention of Clinton's name, and the Republican candidate specifically called for the appointment of a special counsel to investigate the Clinton Foundation.
"Let's call this what it is: A sham," Hillary Clinton spokesman Nick Merrill said Friday in a statement. "This is a philanthropy that does life-changing work, which Republicans have tried to turn into a political football. It began with a long-debunked project spearheaded by [former Trump adviser] Steve Bannon during the presidential campaign. It continues with Jeff Sessions doing Trump's bidding by heeding his calls to meddle with a department that is supposed to function independently. 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. It's disgraceful, and should be concerning to all Americans."
The calls for a special counsel to investigate Clinton-related matters and the FBI have intensified on the right as a separate investigation, led by special counsel Robert Mueller III, explores whether the Trump campaign coordinated with the Kremlin to influence the 2016 election, and whether Trump himself might have tried to obstruct justice in that inquiry.
The Clinton Foundation has raised billions of dollars since it was formed and generally receives high marks from philanthropy watchdog organizations. But because of its global donor base and Hillary Clinton's former position as the United States' top diplomat, it also faced questions about contributions from countries such as Saudi Arabia, Qatar and Algeria.
