It includes reports that Myanmar's national police chief, Major General Khin Ye, had "personally supervised the brutal arrests, beatings and killings of monks" at Yangon's Shwedagon Pagoda on September 26.
"Harsh repression continues, and the government is still lying about the extent of the deaths and detentions," Brad Adams, HRW's Asia director, said in a statement noting the crackdown was "far from over".
HRW says the report was based on interviews with more than 100 eyewitnesses in Myanmar and Thailand, including several Buddhist monks who formed the vanguard of the street protests against the military government.
Describing a raid on his monastery, one monk, U Khanda, said his head was injured after he was hit by baton charges while dozens of his fellow monks were taken into detention.
"I saw pools of blood, shattered windows, and spent bullet casings on the floor when I came back to the monastery in the morning," he is quoted as saying.
"We found about 100 monks missing out of 230 monks."
Another eyewitness, Zaw Zan Htike, who was in Yangon, said soldiers began shooting immediately after warning people to disperse.
"Twenty soldiers came over the barricade, climbed over, and started beating the people. Two people died. … It was not like in the movies. When the soldiers beat those people, they were trying to kill them."
Although the most international attention was focused on the crackdown was in Yangon, the former capital and the country's biggest city, HRW says the toll was much higher given the killings and detentions in other cities and towns.
"The generals unleashed their civilian thugs, soldiers and police against monks and other peaceful protestors," Adams said. "Now they should account for those killed and shed light on the fate of the missing."
Calling for greater international pressure on Myanmar's military government, HRW criticised the lack of action by Myanmar's trading partners and neighbours.
Adams said countries like China, India and Thailand should try to hold Myanmar's generals accountable and end military repression in the country.
"It's time for the world to impose a UN arms embargo and financial sanctions, to hurt Burma's [Myanmar's] leaders until they make real changes," he added.