The State's regulator for housing bodies has appointed inspectors to carry out a statutory investigation into the Peter McVerry Trust.
The Approved Housing Bodies Regulatory Authority (AHBRA) says it was first notified of a number of financial and governance issues at the housing charity in July.
In a statement, the housing regulatory authority said "the appointed inspectors have been asked to prepare and submit to AHBRA a report on their investigation and findings".
It said: "It is important to note that the commencement of a statutory investigation is not in itself a finding of any wrongdoing."
AHBRA said it had determined that a statutory investigation was required having identified concerns in relation to the organisation.
An independent auditor was appointed to carry out a financial and governance review during the summer after the charity said it was facing serious cash flow pressures.
Last month CEO of Peter McVerry Trust, Francis Doherty, said it was "experiencing cash flow pressures that are more acute than would traditionally be the case, even allowing for the summer period".
Services provided by the trust will continue uninterrupted while the investigation is under way.