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 says that the door has now been shut and that the last person has viewed Gaddafi’s body.
The bodies were found on Sunday on the lawn of the abandoned Hotel Mahari in Sirte, which saw heavy fighting last week as NTC forces battled for control of the city.
“Some had their hands bound behind their backs when they were shot,” Peter Bouckaert, emergencies director at Human Rights Watch, said in a statement.
“This requires the immediate attention of the Libyan authorities to investigate what happened and hold accountable those responsible.”
It is not clear who carried out the killings.
HRW said they believed the hotel had been in the hands of anti-Gaddafi forces from Misrata before the killings, and it remained in their control until the fighting in Sirte stopped on 20 October.
On the entrance and walls of the hotel were the names of several anti-Gaddafi brigades from Misrata, HRW added.
“The evidence suggests that some of the victims were shot while being held as prisoners, when that part of Sirte was controlled by anti-Gaddafi brigades who appear to act outside the control of the NTC,” Mr Bouckaert said.
Many of the victims suffered bullet wounds to the head, according to an AFP reporter who saw them.
Human Rights Watch also said the remains of 95 people had been found at the site where Gaddafi was captured. They appeared to have died that same day.
HRW, Amnesty International and other rights groups regularly document incidents of atrocities suspected of being carried out by pro- and anti-Gaddafi forces during the conflict. These include several mass killing sites found in August.
In his speech on Sunday in Benghazi, NTC leader Mustafa Abdul Jalil urged Libyans to put civil conflict behind them for the sake of the country.
“Today we are one flesh, one national flesh. We have become united brothers as we have not been in the past,” he said.
“I call on everyone for forgiveness, tolerance and reconciliation. We must get rid of hatred and envy from our souls. This is a necessary matter for the success of the revolution and the success of the future Libya.”
Mr Abdul Jalil said the new Libya would take Islamic law as its foundation. Interest for bank loans would be capped, he said, and restrictions on the number of wives Libyan men could take would be lifted. Sounds like fundimentalist Mormon heaven to me.