Human Rights Watch (HRW) said the victims - some of whom had their hands bound - died about a week ago.
It is the latest accusation of atrocities in Libya committed by both sides during the eight-month conflict.
Libya's new rulers have denied any involvement in abuses and have urged Libyans to forego reprisal attacks.
The discovery comes a day after jubilant crowds across the country took to the streets as the interim government declared national liberation, three days after the death of Muammar Gaddafi.
The National Transitional Council (NTC) has come under pressure to investigate how the former leader died, following accusations he had been executed by NTC troops after his capture in Sirte.
His body is in a cold storage facility in Misrata.
It has been on public view, but the commander at the refrigeration unit told the BBC that the door has now been shut and that the last person has viewed Gaddafi's body.
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