(CNN) The Justice Department attorneys prosecuting Roger Stone -- who no longer work under special counsel Robert Mueller -- defended the special counsel's investigation of President Donald Trump Friday, saying it inherently did not hamper his ability to lead the country.

The argument came amid a series of filings Friday night in Stone's case, in which prosecutors pushed back on the longtime Trump ally's legal attacks on Mueller and the criminal charges he faces . Stone has pleaded not guilty to the charges against him and asked the court to dismiss them.

"While the Department of Justice's position is that 'the indictment or criminal prosecution of a sitting President would impermissibly undermine the capacity of the executive branch to perform its constitutionally assigned functions,' it also takes the position that a criminal investigation during the President's term is permissible," the prosecutors wrote.

If the Constitution "prevented any investigation of a President or his campaign while he was in office, the government could not preserve evidence while memories are fresh and documentary materials are available. Nor, it would seem, could the government conduct an investigation that may clear the President of alleged wrongdoing."

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