Perth man Aliya Zilic, 33, has been charged with murdering his three-year-old son Imran, believing the child was the devil's helper.

But his lawyer, Bronwen Waldron, has told the SA Supreme Court that Zilic's psychosis "obliterated any sense of what he had done and what he was doing".

Justice Margaret Nyland has been asked to determine if Zilic, 33, was mentally incompetent at the time of the murder to stand trial.

Zilic allegedly killed his son at Coober Pedy in SA's far north between April 20-24 last year, and prosecutors claim he then fled further into the outback.

He was arrested in the West Australian town of Kununurra on May 1 last year, after travelling through outback Northern Territory on a "bizarre odyssey", Ms Waldron told the court yesterday.

Ms Waldron said there was a "religious overlay" to the killing, saying Zilic had been described by family members as a "loving father" considered incapable of harming his son.

Zilic had experienced schizophrenic episodes since 2001 but had stopped taking medication in the months before the killing and had "bizarre oblivionism to the horror of what happened", she said.

Ms Waldron argued Zilic was, due to the mental illness, incapable of controlling his actions at the time.

After the killing, Zilic returned to a Coober Pedy dug out where he had been staying with his son and washed the murder weapon in a "respectful, almost religious cleansing", she said.

He then drove, without trying to conceal his identity or vehicle, throughout the NT and into WA in the actions of a "damaged psychotic man trying to go through the motions of life", Ms Waldron said.

When arrested by police, Zilic denied involvement in the murder, because "when you are speaking with the devil, you don't have to tell the truth", she said.

Prosecutor Jim Pearce has told the court Zilic believed his murdered son to now be in the hands of God.

Mr Pearce on Tuesday said Zilic was mentally ill at the time of the murder but "it's a question of whether he was able to control his actions".

Mr Pearce said Zilic was "a man on the run" and "a man who was trying to lie his way out of trouble" following the murder.

Justice Nyland reserved her decision.