A NSW Health official has accused journalists of trespassing after more than 1000 sensitive patient records were found in an abandoned nursing home.

The confidential medical records were found on the floor of a government aged care facility decommissioned in the early 2000s.

NSW Health Minister Brad Hazzard has promised an investigation into how the files were left behind when patients at the Garrawarra Centre for Aged Care in Helensburgh were moved to a new facility.

ABC reported the files covered more than 400 patients and contained information about specific conditions, treatments and medications.

James Mackie, the medical executive director of the local health district responsible for the nursing home, apologised "unreservedly" to patients affected by the breach situation.

He said the department had repeatedly repaired fences around the building but was until Thursday unaware abandoned medical records were inside.

Dr Mackie said the documents were mixed up with finance documents left behind.

"Due to the latest break-in and trespass by members of the public and ABC staff and in addition to an increase in security patrols, further fencing will be erected to secure this site," he said.

NSW Health has referred the alleged trespass to police.

The department says it will formally notify family members associated with the records - which span from 1992 to 2002 - and commission an audit of archived medical records across the state.

The ABC said it returned the documents to NSW Health on Friday.

The health minister also apologised.

"To those people whose medical records were put in such storage arrangements in the early 2000s, I express my sincere apologies and can assure them and their families I will get NSW Health to do whatever I can to rectify the situation," Mr Hazzard said.

State and territory public health services are generally not covered by the federal government's scheme that forces the reporting of all health data breaches to the Australian privacy commissioner.