They accuse President Bashar al-Assad's regime of crimes against humanity, in a report for the UN Human Rights Council, BBC News reported
The study says both loyalist and anti-government forces have committed possible war crimes.
Many detainees were tortured, some were beaten to death, and others died from lack of food, water, or medical care.
The findings come from interviews with hundreds of witnesses and cover the period since the start of anti-government protests in March 2011.
The report says thousands of detainees have been killed while in the custody of warring parties during that time.
Survivors' accounts "paint a terrifying picture of the magnitude of the violations taking place," it said.
Read alsoSyrian refugee flow can't be stopped until Russia, Assad halt airstrikes: ErdoganFormer detainees described inhuman conditions of detention resulting in frequent custodial deaths.
Officers were observed giving orders to subordinates on methods of torture to be used on detainees.
Corpses were transported by other prisoners through the corridors, sometimes to be kept in the toilets, before being removed from the branch.
Evidence obtained indicates that the superiors of the facilities were regularly informed of the deaths of detainees under their control. Prisoners were transferred to military hospitals before they were buried in mass graves.
Read alsoUp to 20,000 Syrians mass on Turkish borderBoth government and rebel sides are accused of violence against people they detain, the investigators say, but the vast majority are being held by government agencies.
A pattern of arrests since March 2011 targeted Syrian civilians thought to be loyal to the opposition, or simply insufficiently loyal to the government.
