The Commission, a Government reguulator, said there is concern that there is, or has been "misconduct or mismanagement" in the administration of Charr Yarr Welfare Foundation Limited.
A statutory inquiry has now been opened.
The charity is involved in promoting education and the relief of poverty throughout the world but particularly in Pakistan by the establishment of centres of education and the promotion of self sustaining initiatives in impoverished areas, including but not exclusively those relating to farming, manufacturing and health projects .
The regulator opened a compliance case into the charity in April 2018 to examine financial concerns, including the charity being unable to provide receipts for £27,200 of grants made to a partner charity based in Pakistan.
The charity’s accounts for the financial years ending 31 August 2016 and 31 August 2017 were also submitted to the Commission late.
After two compliance visits, the regulator issued regulatory guidance and an action plan to the charity, however the trustees again failed to file accounts for the financial year ending August 2018 on time and continue to be in default of their accounting duties. The trustees were put on notice and advised that this was evidence of mismanagement and/or misconduct in the administration of the charity, the Charity Commission said.
An official warning was issued in January, but since then, the trustees have failed to submit required outstanding financial information and a report in relation to the progress of the action plan, it added.
The charity also remains in default with Companies House in respect of filing the directors’ reports and accounts.
A statement from the Charity Commission said: "The Commission is concerned that action commenced by Companies House to ‘strike off’ the charity from the register of Companies will place the charity at risk of it losing property.
"Despite extensive engagement and attempts to put corrective measures in place, the Commission continues to have serious concerns about the way the charity is run.
"It therefore escalated its engagement to a statutory inquiry on 19 May 2020. The inquiry will further examine the trustees’ governance of the charity in light of their failure to comply with the issued action plan and Official Warning. It will also examine the future viability of the charity."
The Yorkshire Post has contacted Charr Yarr Welfare Foundation for comment.