The National Human Rights Commission (NHRC) said a public inquiry would be held into complaints it had received "bordering on allegations of state-sponsored killings or assassinations".
A newspaper advertisement to announce the probe said it would cover the period from November 1995, when Nigeria was under military rule, to the present day civilian administration.
The formal announcement comes after the military ruler turned civilian head of state Olusegun Obasanjo accused President Goodluck Jonathan of training a private army to carry out political "hits".
Claims will have to be submitted for consideration within three weeks and hearings would be held on a date to be fixed, the NHRC said.
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The organisation's chairman, Chidi Odinkalu, said the inquiry was not a witch-hunt but was designed to deliver justice for those affected by alleged abuses.
"Let's get the issue straight. The investigation is not about individuals. This is a story of victims that don't have remedies," he told AFP.
"It's about institutions that may have committed rights abuses."
Both groups said they had documented a number of cases of extra-judicial and politically motivated killings over the years, particularly around the time of elections.