The Charity Commission has accused Revelation TV of mismanagement and "serious failings" in governance.
Its report, published on Friday, follows a six-year investigation into the popular Christian broadcaster that started in 2014 when the Commission says it was contacted by members of the public who were concerned the charity was being used for private advantage.
The claims have been strenuously refuted by the broadcaster, which has accused the Commission of harassment.
The investigation was launched in the wake of the charity's relocation to Spain, which the Commission said had created an "overly complex" operating structure.
While the Commission said there was no evidence to suggest that charitable funds had been misappropriated, the extent of the failings in structure and governance of the charity "amount to mismanagement" by the trustees.
The Commission claimed that the structure of the charity became so "unwieldy" that it put a "significant proportion" of assets "at risk".
"The complexities in the structure and the flow of funds from the charity to the other entities created a situation whereby substantial inter-company balances became owed to the charity, placing the charity in a vulnerable financial position," the report reads.
The charity and its associated companies were found to be "inadequately separated", and that there was the potential for "conflicts of interest" between the different entities.
Trustees failed to identify and manage these conflicts of interest, the report said, although it added that it had found no evidence of unauthorised benefit on the part of trustees.
The report went on to say that trustees "did not clearly understand their roles and responsibilities", nor the structure and funding of the charity's entities.
"This lack of understanding contributed to a number of significant governance failures including but not limited to the failure to implement and maintain appropriate financial controls, such as were needed to protect the charity's substantial investment in the Spanish broadcasting operation; the failure to conduct detailed risk assessments and obtain appropriate professional advice before taking major decisions; and the failure to properly account for the charity's property by maintaining a detailed asset register," the report said.
Revelation TV also came under criticism from the Commission for failing to seek professional advice before making strategic decisions, and for failing to keep adequate minutes of meetings.
Elsewhere, the report said that Revelation TV founder Howard Conder, although not a trustee, held "significant power and influence over the charity's decision-making process".
The report concluded that Revelation TV "had recognised the regulatory concerns of the Commission and had taken remedial action over the course of the time the inquiry was open".
The Commission has nonetheless ordered the broadcaster to take further action to address its concerns.
"Whilst the highest risk areas resulting from poor governance have been addressed, the Commission is concerned to ensure that the current momentum in progress and improvements is maintained in the longer term," it said.
Responding to the report, Revelation TV said it had been "vindicated" by the findings.
In a statement, Chairman Peter Darg said the Commission's concerns had not warranted a six-year investigation.
"While the length of the investigation was inordinate, it is important to emphasise that Christian charities in the future should not be unnecessarily targeted for unwarranted investigations, and we rejoice that the charity's reputation has been vindicated," he said.
"We can now move on to complete construction of our new international media centre in Mijas, Spain. Throughout the entire investigation process, Revelation TV has continued to broadcast a full schedule of programmes to benefit the public.
"It is just so sad that so much charity money, plus emotion and stress has been expended on an unnecessary investigation."
The Charity Commission defended its findings and denied unfairly targeting a Christian organisation.
A spokesperson for the Commission said: "Our report sets out the findings in our inquiry in full, including the trustees' governance failures and our finding that there was mismanagement. We are not aware of any legal challenge to our inquiry.
"We assess all concerns about charities against a clear regulatory and risk framework, and strongly reject any suggestion of bias in our casework.
"None of the factors we use to assess risk are based on religion. We publish transparency data about our inquiry work, and are clear that our investigations and our casework do not focus on any specific religious classification."