The watchdog has announced it's opened a statutory inquiry into the Revelation Foundation, the group which runs the channel.
In a statement the Charity Commission said: "In March 2014 complaints were received from members of the public alleging the charity was being used for private advantage.
"A subsequent scrutiny of the charity's accounts by the commission identified regulatory concerns which include potential significant loss of charitable funds, trustee benefits, conflicts of interest and connected party transactions.
"These concerns are primarily in relation to the production and broadcasting of television programmes from Spain as well as the trustees' decisions to transfer significant charitable assets and funds from the UK to Spain."
Revelation TV says the statement was unnecessary as it had cooperated fully with every question asked by the Commission.
The channel has responded in its own statement: "We have welcomed the charity inquiry and said we will answer any questions they have about the working of the charity.
"They have agreed to meet with two of the trustees in the next couple of week. But our concern with the press release is the damage it may do to those who look to us as a TV station to give integrity and transparency."
Revelation TV was founded by Howard and Lesley Conder and has been broadcasting for 10 years.
On its website it says the channel broadcasts to millions of households in the UK and Europe via various TV platforms and around the world via the internet.
Gordon Pettie, chairman, Revelation Foundation: