The international human rights group said in a report issued Monday that basic techniques of protecting and investigating crime scenes are not utilized, and autopsies and inquests are either not carried out or are inadequate.
Consequently, family members often can't find out what happened and can't receive justice, the organization said.
Looking at medical and legal sources, Amnesty International said it found that in Rivers state, in southern Nigeria, doctors routinely sign death investigative reports without properly examining the body.
In some cases, the identity of the deceased isn't known and police make little effort to identify them, the report said.
"The lack of investigation in Nigeria means that many of the police officers who appear to have used unlawful lethal force enjoy impunity, seriously undermining human rights protections," the rights group said.
The organization called on all levels of the Nigerian government to investigate all violent deaths, to ensure adequate autopsies were carried out and to prosecute those guilty of the killings.