Hunter Biden's plea deal fell apart during his first court appearance Wednesday morning, as federal prosecutors confirmed the president's son is still under federal investigation. 

The president's son was expected to plead guilty to two misdemeanor tax counts of willful failure to pay federal income tax, as part of plea deal to avoid jail time on a felony gun charge.

But Judge Maryellen Noreika pressed federal prosecutors on the investigation and questioned whether there was the possibility for future charges.

The judge asked prosecutors if Hunter Biden was currently under active investigation. Prosecutors said he was, but would not answer specifically what the president's son is under investigation for.

Prosecutors on Wednesday said Hunter Biden pleading guilty to the two misdemeanor tax offenses would not immunize him from future charges. 

The judge asked whether a potential violation of the Foreign Agents Registration Act was under consideration, but prosecutors were tight-lipped on the matter. 

The judge put the court in recess and asked that federal prosecutors and Biden's legal team discuss the plea deal, telling the court that they did not appear to be in agreement on the terms. 

Hunter Biden was also expected to enter into a pretrial diversion agreement regarding a separate felony charge of possession of a firearm by a person who is an unlawful user of or addicted to a controlled substance.

His plea deal, which has faced ire from Republicans and opponents of the president, was likely to keep Hunter Biden out of jail. 

This is a developing story. Please check back for updates. 

Fox News' Griff Jenkins, Alexandra Rego and Jake Gibson contributed to this report.