The losses have unsettled congregations in what is the fastest growing section of the church in Britain.
It is estimated that more than 150,000 people are members of such churches in Britain, giving more than pounds 50m in annual donations.
Last month a London pastor was jailed for the theft of pounds 56,000 and the Charity Commission is investigating two other churches where thousands of pounds have been reported missing.
The growing problem of unaccountability and corruption in in the churches is featured tonight on BBC 2's Black Britain. Ninder Billing, the producer, said: "It is a really worrying phenomenon. Giving and tithing are integral parts of black worship but some churches are keeping their congregations in the dark about how the money is spent."
She said that anyone could set up a church, start preaching and collect cash.
Many of the evangelical churches have also become registered charities and some are said to be abusing their status.
Stuart Crookshank, regional operations manager at the Charity Commission, said: "In many cases, unfortunately, charities are seen as personal fiefdoms and in cases like that it's normally a recipe for some problem."
The Commission is currently investigating complaints by church members at the Emmanuel Pentecostal Faith Church of God in Streatham, south-west London.
Mrs Ena Hill, a church member, said: "There were donations of pounds 50, pounds 100, pounds 80, various amounts that we just more or less put into an envelope and wrote our name on it and handed it over."
Under charity laws, the head of the church, Pastor Roy Forde, is obliged to open the church's books to church members. They showed that pounds 45,000 in donations made in the last three years had evaporated to a bank balance of pounds 200.
Pastor Forde declined to say how the money had been spent.
In a separate case, the commissioners have frozen the bank accounts of Zoe Ministries Worldwide UK Trust, one of the largest black-led churches in Britain, run from a school hall in Peckham, south-east London. No one at the church was available for comment yesterday.
Pastor George Hargreaves, of the Hepsibah church in Hackney, east London, said that people had a right to question pastors about how their donations were spent but were reluctant to do so.
"Pastors are still leaders in the black community and if you start to knock down your leaders, you're actually knocking down your community," he said.
Last month Pastor Terry Mene received an 18 month jail sentence for fraudulently obtaining about pounds 56,000 after setting up a church at his home in Camberwell, south-east London.
One congregation member said that the church - known as the Celestial Fund for Battered Women and Children - was no more than a front.
She said: "He came here [from Nigeria] and decided to set up a ministry even though he had no religious training ... the only thing that he worshipped was money."