The heavy redactions were expected because the intelligence community now has 12 individuals working full-time at the State Department to review the emails for possible classified material, officials told CNN.
The new measures were put in place several weeks ago, after the Intelligence Community's Inspector General notified the Department of Justice about a potential compromise of classified intelligence from several agencies.
The watchdog also notified Congress about the potential breach after a sampling of 40 of the 30,000 emails sent from her private server found that at least four of them contained classified information, though they had not been identified that way.
In the letter to Congress, IG Charles McCullough said that State Department Freedom of Information Act officials told the intelligence community IG that "there are potentially hundreds of classified emails within the approximately 30,000 provided by former Secretary Clinton."
Because the material was not marked as classified, Clinton may not have known she was handling sensitive material. Clinton has repeatedly denied sending classified information from her personal sever.
The State Department said the new team of intelligence experts was put in place to resolve the issue.
The inspectors general from the State Department and Intelligence Community also told Congress the Clinton's private attorney, David Kendall, is in possession of a thumb drive with copies of the 30,000 emails Clinton has turned over to the State Department.
The State Department said Kendall's firm, Williams and Connolly, has taken "appropriate measures" to secure the material.
Clinton had said previously that she and Kendall screened her emails before handing them over and destroyed any messages that were considered entirely personal.
In a letter to the FBI, Senate Judiciary Committee Chairman Chuck Grassley (R-Iowa) said the thumb drive raises "very serious questions and concerns if a private citizen is somehow retaining classified information."
"It's a serious breach of national security if the United States government fails to secure classified material in the hands of people not authorized to possess it, no matter who they are," he wrote, asking the FBI about the thumb drive and sought more information on Kendall's security clearance and whether he was authorized to be the "custodian of classified national security information."
Alec Gerlach, a State Department spokesman, said the agency was confident that the material would remain secure though he would not detail the steps taken.
"We've provided the lawyers with instructions regarding appropriate measures for physically securing the documents and confirmed via a physical security expert that they are taking those measures," Gerlach told CNN.
The official noted that Kendall has the security clearance necessary to handle such sensitive information. Kendall has represented Clinton and her husband, former President Bill Clinton, since their days in the White House. He also represented former CIA Director David Petraeus against charges of mishandling classified information.