The Charity Commission will look into what it describes as 'serious regulatory concerns' over CAWRM Ltd - known as Jerusalem Merit - the organisation launched after White moved on from FRRME, the charity he founded for his work in the Middle East.
Accusations made by the Commission include unnecessary risks in moving money abroad and unexplained or unauthorised payments to trustees and a private company.
The charity says it is disappointed with the decision by the Commission and claims some of the findings are inaccurate.
While an inquiry takes place, the charity will be required to work under restrictions.
Responding to the decision the trustees of CAWRM said: "We acknowledge the role that the Charity Commission plays in ensuring charities can thrive and inspire trust so that people can improve lives and strengthen society. CAWRM Ltd, also known as Jerusalem Merit, provides much needed support for families from Iraq, who have had to relocate to Jordan as refugees, with no means of financial support, education or basic health care.
"On 10 January 2019 the Charity Commission published a press release in which some of the comments are inaccurate.
"Following an initial visit by the Charity Commission in August we have complied with all of their requests for information and are disappointed that they have taken this approach.
"One of the strategic objectives of the Charity Commission is "giving charities the understanding and tools they need to succeed". As Trustees we have made many requests for guidance and leadership yet we can only identify 3 occasions when they have responded. On each occasion the answer has either been totally unsatisfactory or has conflicted with information that they have provided.
"We are a totally transparent organisation and, as stated, our goal is to aid refugees in Jordan. In doing this we rely heavily on our Ambassador, Canon Andrew White, without whom the charity would not exist, alongside support staff. His global presence has enabled funding to come from across the world and these have helped towards educating children, feeding and clothing refugees and also enabling health and medical care.
"Whilst we acknowledge that there were some initial shortcomings beyond our control the Trustees are of the opinion that there is now adequate Governance and controls in place.
"As part of the Statutory Inquiry we, the Trustees, are reviewing performance, competencies and communication levels and will make recommendations for improvement."
The Charity Commission previously launched an inquiry into White's former charity FRRME over claims he had paid cash to Islamic State terrorists in return for the release of slaves.
He faced a police investigation over the claims - but was completely cleared.
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