The report, which was provided to lawmakers, states, "At a minimum, Secretary Clinton should have surrendered all emails dealing with Department business before leaving government service and, because she did not do so, she did not comply with the Department's policies that were implemented in accordance with the Federal Records Act."
The report examined record keeping laws, policies and practices at the State Department from 1997 to present.
Clinton and several of her staff members during her tenure declined to be interviewed, the report said.
The report draws attention to two staff members in the Office of Information Resources Management, who back in 2010 "discussed their concerns about Secretary Clinton's use of a personal email account in separate meetings with the then-Director" of their office.
The report says, "According to the staff member, the Director stated that the Secretary's personal system had been reviewed and approved by Department legal staff and that the matter was not to be discussed any further." The same director reportedly "instructed the staff never to speak of the Secretary's personal email system again."
But the report notes that interviews with officials from the Under Secretary for Management and the Office of the Legal Adviser found "no knowledge of approval or review by other Department staff" of the server.
Clinton has long maintained that she had permission to use personal email.
She told CNN's Brianna Keilar in July that "the truth iseverything I did was permitted and I went above and beyond what anybody could have expected in making sure that if the State Department didn't capture something, I made a real effort to get it to them."
But the report says that the Inspector General's office "found no evidence that the Secretary requested or obtained guidance or approval to conduct official business via a personal email account on her private server."
In a statement following the report's release, Clinton campaign spokesman Brian Fallon, wrote that "While political opponents of Hillary Clinton are sure to misrepresent this report for their own partisan purposes, in reality, the Inspector General documents just how consistent her email practices were with those of other Secretaries and senior officials at the State Department who also used personal email."
But while the report acknowledges personal email use by previous secretaries, it also notes that the rules for preserving work emails sent from a personal email account were updated in 2009, the year Clinton took office.
The National Archives and Records Administration regulation, according to the report, says that "Agencies that allow employees to send and receive official electronic mail messages using a system not operated by the agency must ensure that Federal records sent or received on such systems are preserved in the appropriate agency record keeping system."
Fallon told CNN's Wolf Blitzer Wednesday afternoon that "at the time that she took office and for the duration of her tenure there, the use of personal email for work purposes was not disallowed."
He attributed issues with retention of emails to "shoddy" record keeping at the State Department.
When asked why Clinton did not accept the inspector general's request to be interviewed, Fallon said that Clinton had prioritized the Justice Department's investigation into the email server.
"We never could quite make sense of why this review by the State Department IG was proceeding on its own timeline in a parallel fashion to the Justice Department review," he said.
Fallon also said the inspector general's office may have exhibited an "anti-Clinton bias."
"There were questions raised about this office during the course of its investigation; there were reports about individuals in this office coming forward and suggesting there were hints of an anti-Clinton bias inside that office," he said.
The department's inspector general was appointed by the Obama administration.
State Department spokesman Mark Toner briefed reporters Wednesday: "While not necessarily encouraged, there was no prohibition on using personal email. The only requirement is that -- and the regulations do state this, that these records need to be preserved."
Department officials told reporters on a conference call that Secretary of State John Kerry had asked the inspector general to undertake this review in March 2015.
The officials said that the department had already decided to accept all eight of the recommendations made in the report.
This is not the first time Clinton's use of a private email has been criticized by an inspector general.
In January the inspector general for intelligence agencies wrote a letter to Congress saying that two government agencies flagged emails on Clinton's server as containing classified information, the inspector general said, including some on "special access programs," which are a subset of the highest "Top Secret" level of classification, but are under subject to more stringent control rules than even other Top Secret information."
At the time a Clinton campaign spokesman alleged that the Inspector General for intelligence agencies had been intentionally leaking seemingly damaging information in collusion with Senate Republicans.
Clinton's campaign and the State Department have long denied that any information was handled improperly, saying that the information and emails in question were all retroactively classified.