Many ex-members disclosed accounts of historical abuse in 2013, after the Jesus Fellowship - formerly known as the Jesus Army invited people to share their personal experiences.
Historic allegations were passed on to police and ten people have since been convicted for various sex offences.
An investigation by the BBC has found that a total of 43 people in the church have been linked to reports of historic sexual and physical abuse, including rapes, bullying, brainwashing, forced labour, financial bondage and beatings.
Members also allege the church decreed that children could be disciplined by any adult, and that many were separated from their parents by the age of twelve or thirteen.
Most of the claims relate to incidents in the 1980s and 1990s.
The church voted to shut down as a national body and revoke it's constitution earlier this year as a result of the various abuse allegations.
The Jesus Army has apologised to anyone "who experienced harm in the past" and has urged victims to contact police.
At its peak, in the early 2000s, the evangelical group is believed to have had more than 2,500 members living in communes in Northamptonshire and various other areas of the country.
In a statement posted on the church website, an apology was given for the "faults and failures" which have had a profound impact on many people's lives.
It said: "We are deeply sorry for, and appalled by the abuse that has taken place within Jesus Fellowship Church and the New Creation Christian Community and offer our heartfelt sympathy and unreserved apology to all those affected.
"Children and vulnerable people were entitled to expect full protection from harm. We acknowledge the pain many of those people continue to feel. As things have become clearer to us, we are grieved and deeply troubled."
A spokesperson for the church has announced that a formal redress scheme is being developed to provide money and counselling for the victims of past mistreatment.
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