In a report on Monday, Human Rights Watch said the Burundian military and opposition forces have committed serious war crimes, including civilian killings and rapes.
The report documents rights abuses between April and November this year, when the government and the main rebel groups signed a peace accord.
It describes how the Tutsi-dominated military deliberately killed scores of civilians during combat in April with Hutu rebel forces near the capital Bujumbura.
And in September the military committed similar killings at Muyira and Ruziba.
During the same period, fighters from the main armed opposition groups - the FDD and the National Liberation Forces (FNL) - killed scores of civilians and pillaged their property.
The report added both government soldiers and rebel combatants have raped women and girls, a crime committed with increasing frequency in the capital and surrounding areas in Burundi.
Proponents of the peace deal have argued the immunity clauses were necessary to bring as many parties as possible to the negotiating table.
But Alison Des Forges, senior adviser to HRW's Africa Division, said agreements based on immunity from prosecution rarely work.
"Civilians who have been attacked... say they have been forgotten. Protecting perpetrators of crimes from prosecution victimises civilians yet again. It deprives them of any justice for what they have suffered"
Alison Des Forges,
Human Rights Watch
She said the 1999 Lom Accord that was supposed to end the civil war in Sierra Leone is one obvious example.
Brutal civil war
"With the recent agreements, government soldiers and FDD combatants have no need to fear being held accountable for their conduct," she said.
"Civilians who have been attacked... say they have been forgotten. Protecting perpetrators of crimes from prosecution victimises civilians yet again. It deprives them of any justice for what they have suffered."
Burundi has been plagued by tension between the dominant Tutsi minority and the Hutu majority since independence in 1961.
The current civil war, ongoing since 1993, has killed an estimated 300,000 people, most of them civilians.