The Charity Commission, who regulate the charity sector, revealed on Thursday that only around half of charities meet the standards required for external scrutiny and they will be now applying a benchmark for basic scrutiny.
It called the findings "concerning", with failings including incomplete reporting of transactions to auditors and saying it "raises additional concerns that the failure by trustees to manage conflicts of interest is also being under-reported."
Trustees of registered charities are required to have an external scrutiny of their accounts if they have a gross annual income of over £25,000 in the financial year. The external scrutiny must be either an independent examination or an audit.
The charity Stewardship encourages giving among believers to Christian causes and help churches monitor their finances.
Stewardship's chief generosity officer, Daniel Jones, told Premier's News Hour the Charity Commission's worries were "a timely reminder for both churches and charities that it's important to make sure we know where our money is going to.
"But also for donors, to say 'do I know where my money is going to and, if I want to know more about where my money is going to, how can I go and find out more about what the charity or church is doing with the money that I give?'"
Other problems common among low income organisations were incorrectly labelled or missing financial statements.
Mr Jones said: "This is all about presenting more information to people so they can make more informed choices about how they give and I hope what it will do, as people start to wrestle with this data and see what information is available, is it will actually give them confidence to give more to the things that they care about.
"A number of changes have been brought in to make sure that charities are reporting on things that the Charity Commission believe will be of interest to donors and I think that's only right and fair."
He added that this was particularly important for churches and Christian charities to accept: "There's a uniqueness to the way that churches and charities operate, there's a relationship of trust that's formed when I choose to make a gift to a charity, I'm saying - if we take a kind of a more secular view - 'here is my money and I now invest it to you to go and do something good with it'. What comes with that is a sense of obligation and responsibility to then be able to tell me what you've done with it.
"Of course in the Christian context we operate to slightly different standards...what I want to see is that the money that I believe God has entrusted to me as a steward, when I pass it to you as the church, I want to know that that stewardship is continuing."
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