The South Australian Government has warned that patient safety will be at risk if it is forced to stop using a crucial software system in country hospitals.

The ABC obtained court documents which reveal the extent of a bitter legal stoush between the Government and the maker of the patient records system.

The system called, CHIRON, is used at 64 country health sites in South Australia, including at the Mount Barker Hospital.

In technology terms, the program is ancient and based on the MS-DOS platform. It was installed in SA hospitals in the early 90s.

In the Federal Court CHIRON's maker Working Systems demanded the State Government stop using it because the licence expired in March last year.

The Government said complying would jeopardise patient safety and there would be a material risk to SA Health's ability to provide an effective health service.

According to court documents the Government argued without CHIRON hospital staff would not have access to critical information such as patient allergies to medication and there was potential for new patient data being lost or incorrectly recorded.

Working Systems said any risk to patient safety was the Government's fault because it had failed to plan and refused to sign up to updated software in 2003.

The company said a licence extension for CHIRON was not possible because it was too old and no longer supported.

Court documents show in 2014 the Government assured Working Systems it was seeking a replacement.

That system known as EPAS, which has been dogged by delays, controversy and cost blowouts. It is currently only operating at three sites, including Port Augusta.

The CHIRON matter is listed for trial in December.