Forensic scientists say homicides could be missed if a Government proposal to give cases to local pathologists goes ahead.
The Ministry of Justice wants complex cases managed by local coronial pathologists.
Last week, Justice Minister Andrew Little told the Association of Salaried Medical Specialists the restructure would go ahead, despite protest.
This restructure reverses the 2005 decision to consolidate the work in a single national forensic pathology service.
Auckland District Health Board oversees the national service, which includes four forensic pathologists in Auckland and one each in Palmerston North, Wellington and Christchurch.
Around the country there are another 32 coronial pathologists, but according to National Forensic Pathology Service spokesperson Dr Paul Morrow, they aren't qualified to handle homicide cases.
"They're trained in performing autopsies in hospital cases with natural deaths," he told Newshub.
He says if the restructure goes ahead police investigations could fail, wrong causes of death could be determined or people could be wrongly accused of homicide.
"If your loved one is murdered or dies of an unusual cause, or even if you're accused of a possible homicide in a case, the autopsy may be performed by a general pathologist who is not qualified to handle such a case."
He said the move would also make it harder to recruit specialists from overseas.
Dr Morrow is calling for Mr Little to make the forensic pathology service exempt from the restructure.
Mr Little has said that the restructure will increase the total number of funded forensic pathologists to 10 fulltime equivalents and three forensic trainee posts, across the four providers.
"I therefore do not intend to intervene in, or to terminate, the ministry's procurement," he said.
Mr Little has been contacted for further comment.