Canon Andrew White created the Foundation for Relief and Reconciliation in the Middle East (FRRME) to help people living in war torn parts of the world like Iraq.
In June he was suspended as the president of the organisation because of "some inaccurate statements I made".
The Charity Commission launched an inquiry into suggestions that FRRME had paid cash to Islamic State terrorists in return for the release of slaves.
"What is clear is that at no time did we pay money to any terrorists," said Canon White at the time.
The Charity Commission confirmed it had launched an inquiry but told Premier it cannot comment further because the investigation is live.
In his first major interview since suspension he told Premier it had been "really difficult but I still keep going and we hope that one day it will be back to normal".
He said: "There is concern from the charity commissioners that I may have paid money to terrorists to get back Yazidi and Christian girls who were kidnapped as sex slaves by ISIS [Islamic State].
"I personally did not, but somebody I knew did and we were therefore paying for them to be rehoused and restored and helped and all that wasn't official."
His charity, he said, was providing schools, a clinic and a hospital for refugees who had fled to Jordan from Iraq.
Canon Andrew White has Multiple Sclerosis and said his health had been "difficult and challenging, but I keep going".
He said he would "go absolutely mad" if he had to take more time out to relax.
FRRME's accounts for 2014 show it made £3,032,097 and spent £1,879,670. It has seven members of staff.
Canon Andrew White speaking to Premier's Cindy Kent: