Soldiers killed 22 suspects in a warehouse south of Mexico City in June 2014 in what the army initially described as a shootout.
But the attorney general's office said in October that eight of the suspects were killed by three soldiers after the confrontation had ended.
Another four soldiers were charged with crimes against public service.
The governmental National Human Rights Commission said at least 12 suspects were killed after giving themselves up.
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The commission said the decision is the result of its own investigation, which determined "the existence of several human rights violations."
It did not say how many relatives will share the money but an official told AFP on condition of anonymity that the commission will compensate 13 families which will each receive different amounts.
Authorities are also investigating 20 officials from the central State of Mexico prosecutor's office over allegations that witnesses were tortured in the Tlatlaya case, known by the name of the town where the killing happened.