The Foundation for Relief and Reconciliation in the Middle East (FRRME) was set up by the Church of England priest in 2005 as a way of supporting those affected by war in the Middle East as well as promoting inter-faith dialogue.
Its work across the region has been widely commended but earlier this year the Charity Commission launched an investigation into the organisation with some reports suggesting improper use of charity funds.
While the Commission did not give further details, Mr White said it related to the charity's work with girls taken by Islamic State to work as slaves.
Speaking to Premier in September he said it had been "really difficult but I still keep going and we hope that one day it will be back to normal".
In a Facebook post on Friday, Canon Andrew White confirmed he was leaving FRRME and starting a new organisation called Jerusalem Middle East Reconciliation International.
"JM for short will not be a registered charity because that places on us too many restrictions," he said. "We will still keep supporting and providing for many of our present projects such as the School in Jordan. Which we are committed to totally fund.
"We have a new wonderful partner 'Operation Blessing' led by Pat Robertson and the 700 Club.
He says the organisation will begin immediately and is currently looking at how it can financially support staff.
FRRME told Premier it had been informed Canon Andrew White had stepped down because of ill health and its work supporting refugees will continue.
The Charity Commission has confirmed to Premier its investigation is ongoing.