Blood test samples from the Bain house were lost in a laboratory several years after the killings of five family members, the High Court in Christchurch has been told.
David Bain, 37, is being retried for the murders of five members of his family.
The Crown says he shot his father Robin, mother Margaret, brother Stephen and sisters Arawa and Laniet in their Dunedin home on 20 June 1994.
The defence says Robin Bain killed the family members before shooting himself.
The trial ended its fourth week on Friday, with the defence criticising the forensic handling of the case, saying some of the examination was sub-standard.
The court heard evidence from forensic scientist Peter Cropp, who was working for Environmental Science and Research, but has since retired.
Dr Cropp was asked by defence lawyer Hellen Cull what had happened to blood test slides when the defence asked to look at them in 1997.
Dr Cropp said he understood they had been lost in the laboratory some time after he had left ESR. He said he was quite shocked that the slides had gone missing.
Blood spots on curtain inconclusive
Dr Cropp told the court that blood spots on a curtain near Robin Bain's body could not indicate the point of impact when he was shot.
Dr Cropp was asked to re-evaluate the curtain in the lounge in 1997 and deduced that Robin Bain's blood had been projected from an area of less than a metre above the floor.
Cross-examined by Ms Cull, he said his calculations did not indicate the height at which Robin Bain was shot and the blood may have come from his head as he fell.
The Crown says David Bain shot his father from behind the curtain as he knelt to pray.
The court was told a blood drop on Robin Bain's fingernail could have been tested using modern methods if it had been kept.
The defence contends some blood samples from Robin Bain may have exonerated David Bain if they had been tested.
Under cross-examination, Dr Cropp agreed that it may have been possible to test a blood droplet from Robin Bain's fingernail if it had been collected.
The court was also told blood stains on David Bain's socks could have come from walking on a bloody surface.
On Thursday, Dr Cropp said the blood on one of the accused's socks could have come from either of two siblings, Stephen or Laniet, and appeared to have dropped on the sock. But when cross-examined on Friday, he said another explanation was possible.
The trial will continue next week with evidence from the pathologist who attended the crime scene.