Wilmington, Delaware - President Joe Biden's son Hunter pleaded not guilty to minor tax offenses Wednesday as a deal with federal prosecutors crumbled in a Delaware court.

The surprise move came after Judge Maryellen Noreika raised questions over the original deal – under which Hunter Biden had agreed to enter a guilty plea and admit to illegal gun possession – and effectively placed it on hold.

Biden (53), whose legal troubles have cast a shadow over his father's reelection campaign, had reached an agreement with prosecutors that he would be sentenced to probation on two tax avoidance counts.

The deal also specified that the firearms charge would eventually be erased if he adhered to a counseling-and-rehabilitation program.

But the deal fell apart after Noreika queried why the gun charge was included in a tax case, and whether the plea agreement protected Biden from charges that might arise from a wider ongoing investigation of his business dealings, according to US media.

When prosecutors could not resolve her questions, Noreika said she could not accept the deal, and Biden then entered a not guilty plea to close the session.

That was expected to send the deal back to negotiations, which could become more complex. Noreika gave the two sides 30 days to report back on where they stand.

Meanwhile prosecutor David Weiss confirmed to the court that his office is still examining other possible crimes by Biden, without offering specifics.

One issue mentioned in the court was possible violation of the Foreign Agents Registration Act, relating to Biden's business deals in China, Ukraine, and other countries dating back to the early 2010s, when his father was vice president.

The unexpected collapse of the arrangement came after Republicans accused Weiss of giving Biden a "sweetheart deal" with the plea agreement announced on June 20.

White House Press Secretary Karine Jean-Pierre said Wednesday that Hunter Biden was "a private citizen. This was a personal matter."

The case was "handled independently by the Justice Department under the leadership of a prosecutor appointed by President Trump," she added.

The plea deal was to end a five-year investigation that Republicans have sought to use to politically harm his father Joe.

According to the charges, Hunter, a Yale-trained lawyer and lobbyist, failed to file his tax returns on time on earnings of more than $1.5 million for 2017 and 2018. He was facing up to 12 months in prison for each tax charge and a possible maximum 10 years on a charge that, as a known drug user, he had illegally possessed a handgun in 2018.

But prosecutors recommended probation on the tax charges after Biden paid the taxes and penalties, according to his attorney.

In addition, the gun charge was to be suspended and then eliminated if Biden completed "pretrial diversion," which often involves counseling or rehabilitation.

That would require Biden to remain sober as the charges arise from a long period when he says he struggled with addiction to alcohol, crack cocaine and other drugs.

Late Tuesday, Republicans sought to influence the sentencing, presenting a sealed submission to the court by Representative Jason Smith, the chairman of the House Ways and Means Committee.

Smith's committee has recently taken testimony from whistleblowers from the Internal Revenue Service who alleged that political interference prevented a fuller probe of the president's son.

But Weiss has rejected that claim, and offered to testify to their committee in late September or October, an apparent indication that he sees any other investigation activities regarding Biden to be completed by that time.

At the White House, reporters pressed Jean-Pierre about the case and the Republican investigations in Congress alleging President Biden and his son had illicit business dealings abroad several years ago.

She said the two had no business links and that Biden had no role in Hunter's court case.

"The president, the first lady, they love their son and they support him as he continues to rebuild his life," she said.

In Congress, Republican House Speaker Kevin McCarthy suggested Hunter Biden's case was treated lightly.

"There shouldn't be two justice systems in America," he told reporters.