The filing obtained by AFP yesterday came in response to legal action filed by Judicial Watch, a conservative monitoring group that wants access to all of Clinton's e-mail while she was the top US diplomat.
"There is no question that former Secretary Clinton had authority to delete personal emails without agency supervision -- she appropriately could have done so even if she were working on a government server," the Justice Department wrote in a document filed this week in US District Court in Washington.
Under US National Archives State Department policies, "individual officers and employees are permitted and expected to exercise judgement to determine what constitutes a federal record," the DOJ said.
Judicial Watch President Tom Fitton dismissed that argument as having "absolutely no merit."
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"All we ask is that the court preserves those emails ... until the legal issue is resolved," Fitton told AFP.
"That's up for debate. She set up this system to conduct all of her government business and then she just took it without prior review. And now the government is saying that she has the (unprecedented) right ...To go into this system, and take out what she thinks is personal and leave whatever she thinks is government."
According to Fitton, the Justice Department "is undermining its own investigation of this issue while also providing a defense for Mrs Clinton personally," a move that he said also "benefits her political aspirations."
The Washington Post reported yesterday that the company that managed Clinton's private e-mail server said it had "no knowledge of the server being wiped," suggesting that deleted emails could be recovered.
The scandal broke in March, and it wasn't until this past week that Clinton publicly apologised for using her private e-mail server.
"That was a mistake. I'm sorry about that. I take responsibility," she said in an interview with ABC News.