The man, aged in his 60s, was charged with murder yesterday afternoon.
He was in an intensive care unit bed yesterday, where Judge David Robinson conducted a bedside hearing.
Such instances are rare.
Judge Robinson — who would usually be dressed in his robes and sat far from the defendant — stood next to the man and introduced himself.
The defendant, who did not talk during the hearing, gave a nod and a thumbs up to indicate he could hear and understand the judge.
Judge Robinson suppressed the defendant’s name as well as details of his injuries and any treatment he had received so far.
The defendant’s lawyer, Meg Scally, a police prosecutor, a senior sergeant, a court registrar, two court security staff and a uniformed policeman were also in attendance.
The defendant did not speak and communicated via a whiteboard.
"It’s all overwhelming," he wrote at one stage.
He did not enter a plea to the charge.
Ms Scally said her client was not seeking bail so would be formally remanded in custody, although he would remain in hospital due to his condition.
She did not expect he would be out of hospital any time soon, she said, but did not detect any issues with his ability to give instruction.
He had been taken to hospital in critical condition after Dr Clark was found dead in her home last month.
The Otago Daily Times understands Dr Clark was stabbed.
Following her death, bunches of flowers were laid at the foot of a sign reading "The Country Vet" outside the woman’s Crichton home.
A neighbour and relative, who did not wish to be named, earlier said Dr Clark’s father, Jasper Clark, died at the nearby family farm just a week earlier and she had delivered a "heartfelt" eulogy at his memorial service.
The family was in "utter shock and disbelief" at the incident, which had happened to a "wonderful woman, with no enemies anywhere", he said.
"She was an unfailingly generous, big-hearted person, who always had a smile on her face.
"As a vet and as a person, she loved her animals, put her heart into her job and loved to help others."
Neighbours, family and former colleagues all spoke of a warm, capable and well-respected woman, who was inseparable from her two fox terriers.
Dr Clark had no children of her own, but was described as a beloved aunt to younger family members, inspiring some to take an interest in veterinary science themselves.
"Everywhere Jillian went, the dogs went.
"If you saw her on the farm on her side-by-side, or in her car driving down the road, she’d have the dogs next to her, or on her lap," a family member said.
