Life Line Missions was already being looked into as part of its double-defaulter class inquiry in 2013.
An inquiry has found that the charity's bank accounts had been closed and "substantial discrepancies with income and expenditure" were found.
The Charity Commission, the independent regulator for charities in England and Wales, checks that charities work effectively amongst society to benefit the public.
According to the regulator, Life Line Missions aims to advance the Christian religion and the relief of poverty.
It has failed to file its accounts for the financial years ending March 2011 and 2012.
Additionally the Commission contacted the charity's trustees in winter 2013, but did not "receive acceptable responses".
The inquiry used its power to get information directly from the bank that the charity deals with.
It found that Life Line Missions account was closed in December 2013 and that there were "substantial discrepancies" in the accounts, annual returns and bank statements.
A new inquiry was opened last year.
According to the Register of Charities the charity's accounts from 31 March 2011 are 1,541 days overdue and its 31 March 2012 accounts are 1,175 days overdue.
It did not file accounts for the year ending March 2013, and was not required to file accounts in 2014 at its income and spending fell below the £10,000 threshold.
A Charity Commission spokesperson said while the charity no longer seems to be in operation, the regulator is concerned as there has been "money going through the charity in the last couple of years" that is not accounted for.
They are also worried that it is only registered to one person.
Premier has attempted to contact charity bosses for comment.
