The probe will now look into whether the Swiss bank's French subsidiary intimidated Nicolas Forissier, the whistleblower behind claims that led to a formal investigation into whether the bank was helping clients dodge tax, a claim which the French subsidiary of the Swiss bank has denied.
In a statement emailed to CNBC Thursday, UBS France rejected allegations it was tampering with the witness.
"UBS France confirms that, following a complaint filed by a former employee, the judge decided to put the bank under formal examination...for intimidation of the witness, but not for moral harassment, also alleged by this former employee," the statement read.
"We strongly deny these allegations and are confident that we can vigorously defend our rights and position."
Forissier's lawyers did not provide a statement to CNBC when contacted but reiterated statements made to French media that this was the first time a major bank has been probed in by French prosecutors for pressuring a whistleblower.
Forissier himself was not immediately available for comment when contacted by CNBC.