A U.N. panel of experts, which has been investigating abuses in Syria, has gathered a "massive" amount of evidence indicating such crimes were committed, said Navi Pillay, the U.N. high commissioner for human rights.
"The evidence indicates responsibility at the highest level of government, including the head of state," Pillay said at a news conference in Geneva.
The charge came as a Syrian opposition human rights group said that nearly 126,000 people had been killed since the beginning of the uprising against Assad's government in 2011. The dead include more than 44,000 civilians, according to the British-based Syrian Observatory for Human Rights, which tracks daily casualty tolls in the country.
The U.N. said in July that the death toll had probably surpassed 100,000.
The U.N. commission of inquiry gives Pillay lists of suspected criminals that will remain under seal until they are requested by international or national authorities for a "credible investigation" and possible prosecution, she said, according to the Associated Press.
Although Pillay referred to Assad, it wasn't clear whether his name was on any of the lists. She said the lists must be kept secret "to preserve the presumption of innocence" until proper investigations are launched.
The U.N. panel has not been allowed to conduct investigations inside Syria and instead relies on interviews with refugees and phone or Skype conversations with people in the country.
The panel has documented the growing brutality of the conflict, including massacres said to have been perpetrated by Assad's government as well as opposition forces. On Monday, Pillay said the scale and viciousness of the crimes committed in the war almost defy belief, AP reported.
The Syrian conflict has spilled over into neighboring countries with similarly volatile mixes of religious sects and political affiliations.
Sectarian tensions exacerbated by the Syrian crisis flared over the weekend in the northern Lebanese city of Tripoli, where 12 people were killed and dozens were wounded, according to state media accounts.
It was the latest in a series of clashes pitting supporters of Assad, who is a member of the Alawite sect, an offshoot of Shiite Islam, against Sunni Muslims, who dominate the Syrian opposition.
In response, the Lebanese government instructed the army to take "the necessary precautions to preserve security in Tripoli for six months," the country's caretaker prime minister,
Special correspondent Nabih Bulos in Beirut contributed to this report.