By Stephanie van den Berg and Anthony Deutsch

THE HAGUE (Reuters) - The prosecutor of the International Criminal Court, Karim Khan, has stepped down temporarily as an investigation by the United Nations into alleged sexual misconduct by him nears its end, his office said on Friday.

The move is unprecedented and there is no clear procedure for replacing Khan. The situation creates added uncertainty for the ICC, which is already facing an existential crisis due to U.S. sanctions over its arrest warrants for Israeli officials. 

Khan's office said the prosecutor had taken leave until the end of the investigation by the UN Office of Internal Oversight Services.

The ICC's two deputy prosecutors would take over his duties in the meantime, it added.

Khan's lawyers did not immediately respond to a written request for comment.

  The prosecutor has denied allegations of misconduct that were reported to the court's governing body in October last year.

When the allegations against Khan emerged, several NGOs and ICC staff members called for the prosecutor to step down temporarily for the duration of the investigation, but he initially stayed on. 

Sources, who spoke on condition of anonymity to discuss a sensitive matter, told Reuters that Khan had spoken to U.N. investigators last week in what was believed to be the final interview of a months-long outside investigation into the allegations that started in December.  

It was unclear when the probe would finish.

The ICC has high-profile war crimes investigations under way into the Israel-Hamas conflict and Russia's war in Ukraine.

At Khan's request, the ICC issued arrest warrants for President Vladimir Putin on suspicion of deporting children from Ukraine, and for Israeli Prime Minister Benjamin Netanyahu for alleged war crimes in Gaza. Neither country is a member of the court and both deny the accusations and reject ICC jurisdiction.

The ICC's investigation into Israel's conduct led the U.S. administration of President Donald Trump to impose sanctions on Khan, which the ICC president says have put the court itself at risk. 

(Reporting by Stephanie van den Berg and Anthony Deutsch; Editing by Bart Meijer, Timothy Heritage and Alex Richardson)