The Charity Commission said it had "serious" concerns about the financial information it had received from Croydon Tabernacle - a registered charity.
In a statement released on Tuesday, officials said: "The Commission examined the charity's financial information and found cause for serious regulatory concern.
"This included substantial unexplained expenditure and potentially conflicted payments to people connected with the charity.
"As a result of its concerns, the Commission has frozen a bank account controlled by the charity."
The Charity Commission placed Croydon Tabernacle under statutory investigation, saying previous "engagement" with the church since November 2016 "did not resolve the regulatory concerns".
Investigators shall examine where misconduct, poor administration, breaches of trust or non-compliance with charity law have taken place.
A Croydon Tabernacle spokesman told Premier in a statement: "Our Board of Trustees has received a notice of statutory inquiry from The Charity Commission. We have been assisting fully with their inquiries and, under their guidance, we will take appropriate action to make sure we are compliant."
"We would like to thank our tireless army of volunteers for their hard work within our congregation, our local community and far beyond. We appreciate their patience and understanding while this inquiry takes place."
The church is part of the Nigeria-founded Redeemed Christian Church of God movement.
The Commission will publish a report detailing its findings in due course.
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