Roger Stone checks his phone while posing for this portrait in his office in Oakland Park, Fla., in 2017. (Andrew Innerarity/For The Washington Post)

A federal judge Thursday pushed back on arguments that Trump confidant Roger Stone cannot be charged for lying to Congress without a referral by lawmakers for prosecution, as Stone’s attorneys faced skeptical questions over several of their arguments to toss his case.

Stone, 66, has pleaded not guilty to charges he lied to Congress, obstructed justice and tampered with witnesses in special counsel Robert S. Mueller III’s probe of Russian interference in the 2016 presidential election.

He faces trial in November about his alleged efforts to gather information about Democratic Party emails hacked and leaked by Russian operatives during the 2016 presidential campaign. During a nearly three-hour hearing, his attorneys lodged multiple challenges to his January indictment, including a novel constitutional argument that the Justice Department improperly funded Mueller’s office using money Congress set aside for “independent” instead of “special counsels.”

In making his argument over Congress’s role, Stone attorney Robert C. Buschel said it is up to Congress to enforce its own rules and decide when to vote and formally refer people for prosecution, arguing that anything less violates the constitutional separation of powers between the legislative and executive branches.

But prosecutor Aaron S.J. Zelinsky said that far from the defense’s portrayal of prosecutors trolling the halls of Congress looking for a case to bring, it was Stone who first drew public attention to the veracity of his own testimony when he spoke to reporters after leaving the House intelligence committee and said, “There are those who don’t buy what I’m selling.”

U.S. District Judge Amy Berman Jackson said Congress made clear that prosecutors can enforce a law that makes lying to Congress a crime.

“I don’t understand how it offends the separation of powers,” Jackson said, noting that the then-Republican led House intelligence committee gave its hearing transcripts to the Justice Department with “no restriction on their use” by Mueller’s team or other department offices. “Why is that not the end of it?. . . . They gave it to a prosecutor.”

Jackson made no decisions Thursday and did not say when she would rule on Stone’s motions, after taking the arguments under advisement.

Stone’s defense team continues to ask Jackson for an unredacted copy of Mueller’s 448-page report and they are asking her to find that an appeals court ruled wrongly when it upheld the validity of Mueller’s appointment as special counsel.

During the hearing, Jackson had also challenged Stone’s argument that his indictment violated the Constitution’s appropriations clause. Stone’s attorneys argued that Congress under a 1987 law authorized the Justice Department “to pay all necessary expenses of investigations and prosecutions by independent counsel,” and that they interpret that to mean prosecutors wholly independent of the U.S. attorney general.

Stone attorney Bruce S. Rogow argued that because Mueller was appointed special counsel under rules the Justice Department set up after the independent counsel law expired in 1999,Congress should have changed its funding law.

Rogow cited a ruling last week in which an Oakland, Calif., federal judge temporarily blocked spending for part of President Trump’s border wall plan by finding Congress did not specifically appropriate funds for it.

Assistant U.S. Attorney Adam C. Jed, like Zelinsky a former member of Mueller’s team, said the Justice Department has repeatedly paid other special counsels under the statute, that Congress has approved the long-standing practice, and that in legal circles the term “independent counsel” has regularly been used to describe attorneys, like Mueller, specially named to conduct sensitive investigations with assurances of independence.

Jed cited the department’s funding of special counsels appointed in 1999 to investigate the events surrounding a law enforcement assault on a religious group’s compound in Waco, Tex., and in 2003 to investigate the leak of the identity of CIA employee Valerie Plame.

Jackson appeared to concur with Jed, saying, “I keep coming back to the statute, which doesn’t use ‘independent counsel’ as a term of art, and capi­tal­ize it. It specifically says ‘appointed pursuant to [the Ethics in Government Act] or other law,’ ” punctuating her comment with air quotes.