The commission has also instructed the trustees not to part with any funds from the charity without its permission.
This follows allegations of international baby trafficking made in the press against the charity.
Simon Gillespie, director of operations at the Charity Commission said: ‘The allegations raised in the press are extremely serious, and the Charity Commission will take action wherever charity funds or beneficiaries are at risk.
‘We have examined and considered all the material we have obtained, and feel that we have no choice but to move to an inquiry. We will now be working closely with all relevant agencies to get to the bottom of these allegations.’
The inquiry will examine the activities of the charity and its use of funds. It will also look at the charity’s fundraising and publicity material.
Gilbert Deya Ministries declined to comment.
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