The spokesman, Mark Toner, told reporters that "the people who may have had a broader knowledge or a fuller appreciation of -- to the extent at which Secretary Clinton was using her personal email -- are no longer here at the department."
He added, "They are now, many of them, with Secretary Clinton. And frankly, I would just have to ask you to ask them to answer that question: Whether it was how much they knew? And if they knew that she was relying significantly or solely on personal email, why didn't they make this -- others aware of it? I just can't answer that question."
Clinton told CNN's Wolf Blitzer Thursday that "personal email use was the practice under other secretaries of state, and the rules were not clarified until after I had left."
But, she added, "As I have said many times, it was still a mistake. If I could go back, I would do it differently."
"I believed it was allowed, but that's not the point. I've said it was a mistake," Clinton added.
In the first of at least seven depositions pertaining to Clinton's email usage, the former State Department deputy executive secretary, Lewis Lukens, revealed that Clinton's staff told him that she was "not adept" at using a computer and that the staff had sought a special room to enable BlackBerry access.
The depositions are part of a Judicial Watch lawsuit focused on the department's handling of Freedom of Information Act requests.
This information comes to light as the State Department Inspector General issued a report criticizing Clinton's email practices.
In the exchange, Lukens discussed how Clinton's then-chief of staff, Cheryl Mills, had talked to him about allowing Clinton to maintain access to her email even though mobile devices, including her BlackBerry, were prohibited from being used in her office due to it being a secured facility.
Mills will be deposed Friday at an undisclosed location for up to seven hours. She persuaded a judge Thursday to prevent Judicial Watch from releasing video of the deposition, so a transcript will be made public soon after her deposition concludes.
Lukens, who described his role as "logistics and management support," said he thought Clinton wanted access to private email "for her to stay touch with family and friends" and not for official business.
He revealed how he had offered to set up a dedicated desktop computer in Clinton's office that would not be connected to the State Department's communication systems.
Lukens said he opted for this solution because although personal email could be checked on standard government computers connected to the department's system, he described the process as "cumbersome" because passwords had to be changed every eight to 12 weeks. He said the proposed computer for Clinton would not require a password.
In response to his proposal, Lukens said Mills told him that Clinton was "very comfortable checking her emails on a BlackBerry but she's not adept or not used to checking her emails on a desktop."
Judicial Watch, a conservative legal watchdog group, asked to interview Lukens because of an email exchange he was party to, which they obtained from the State Department earlier this year.
The group has filed more than a dozen Freedom of Information Act lawsuits against the State Department in the past year.