Almost £900,000 of payments to contractors at the Northern Health Trust could be irregular, it was revealed.
Health Minister Edwin Poots is overseeing an investigation into whistleblower reports of potential malpractice in the procurement and management of building maintenance in the area.
The minister told the Assembly: "Although a report has not yet been finalised, it is apparent that there are a number of procurement control weaknesses in the trust's estates function and investigations are still ongoing.
"In this respect, external audits, as part of their audit on the 2012/13 annual accounts, have identified £860,000 of payments in respect of measured day term contracts, which may be potentially irregular due to procurement issues."
The contracts mean a firm undertakes to carry out work which is measured and valued at agreed rates.
Mr Poots added: "The trust has already moved to take some corrective action and health estates investment group, within my department, will also undertake a series of compliance checks across all trusts and further audits are planned for 2013."
He said his department was ensuring all allegations were rigorously investigated so that when any necessary improvements have been made the public can have full confidence in estates procurement practices.
"It is appropriate and important that where anyone has information about abuse of public money this is brought to light so that the specific issues can be resolved, appropriate lessons learned, and public confidence restored," he added.
"Where wrongdoing has occurred it must be addressed, with a proportionate and appropriate response."