The Charity Commission has opened an inquiry into the National Bullying Helpline.
A spokeswoman for the organisation, which regulates charities in England and Wales, said it had received 160 complaints about the helpline this week.
Its founder Christine Pratt provoked a political storm by claiming on Sunday it had received calls from Downing Street staff to seek help over alleged bullying at work.
The commission's spokeswoman said: "Concerns have been raised about the protection of confidential information held by the charity as a result of the operation of the charity's confidential helpline for victims of bullying.
"The commission has a statutory responsibility to promote public trust and confidence in charities, and is aware of the potential impact on other charities that run confidential helplines."
The inquiry will look at the helpline's procedures around data protection and examine how people were referred from the helpline to a business run by one of its trustees. The helpline was temporarily suspended on Thursday.
In a statement, the charity said it was considering its future and announced Mrs Pratt was "prepared to resign if necessary".
A number of the charity's patrons, including Conservative MP Ann Widdecombe, resigned in protest at what they saw as her breach of her duty of confidentiality towards callers.
In a statement on its website, the Helpline said: "Our patrons have resigned at a time when we needed them most. It is a shame that not one of them ever visited our charity offices to see how we operate or meet with our volunteers and trustees, despite request.th 20
"Competitor anti-bullying charities, individuals with an axe to grind and a few others have forced our hand. We are extremely sorry for any distress this may cause to those who need help right now. We apologise also to those who are detrimentally affected by this situation - we include all charities doing very good work across the UK."