A Sydney judge has found a gas company is not responsible for the actions of a "disobedient" contractor involved in a fatal gas mix-up at Bankstown-Lidcombe Hospital.

Key points: A judge found BOC Limited were not to blame for the gas mix-up

A judge found BOC Limited were not to blame for the gas mix-up Contractor Christopher Turner completed paperwork without performing the tests

Contractor Christopher Turner completed paperwork without performing the tests Mr Turner today expressed his "deepest sorrow" to the affected families

In 2016, nitrous oxide was mistaken for oxygen during resuscitations, and newborn John Ghanem died, while Amelia Khan was left with permanent brain damage.

There are now two court cases as a result of the incident — one against BOC Limited and another against contractor Christopher Turner, who installed the pipes.

SafeWork NSW alleged BOC had failed its duty under the Work Health and Safety Act, but the company pleaded not guilty.

In July 2015, Mr Turner and NSW Health assistant engineer Paul Brightwell completed BOC test forms that recorded results for oxygen, air and suction outlets in the hospital's operating theatres.

The results indicated there was "100 per cent" oxygen flowing from the oxygen pipe, the NSW District Court heard.

Judge Wendy Strathdee today said she believed Mr Turner falsified the records by completing paperwork without performing the testing.

The mix-up saw the hospital confuse nitrous oxide for oxygen. ( Supplied )

Mr Brightwell, meanwhile, had signed off on the forms as having witnessed the testing when he had not done so, and was therefore complicit.

"The combination of the falsification of the documents by Mr Turner and Mr Brightwell had the most disastrous and tragic consequences," the judge said.

The matter was complicated by the initial mislabelling of a gas pipe carrying medical nitrous oxide as containing oxygen during 1996 renovations.

But BOC argued if the testing procedures had been followed, mistakes would have been evident and the risk eliminated.

Judge Strathdee found the babies were put at risk by "the lies by Mr Turner and Mr Brightwell".

"The defendant cannot be held responsible for the behaviour of a disobedient worker," she said.

The separate case against Mr Turner, in which he has pleaded guilty, today heard an offer of his "deepest sorrow" to the court and the families.

"He conveys that knowing full well that his heartfelt deepest apology cannot undo or in any way compensate for the tremendous grief and sorrow felt by the families," his barrister Patricia Lowson said.

Mr Turner's sentence will be handed down at a future date.