The Irish Examiner reports that the addiction charity is being investigated by the Data Protection Commissioner regarding a complaint into management, while the Charities Regulator has also issued a direction.
A major financial audit is also being carried out by the HSE, while a large number of protected disclosures were made by staff against the management of the charity.
The charity's CEO Patrick Relihan resigned in June.
Matt Talbot Addiction Services has been in operation in the city for over 20 years.