Alston praised a recent military investigation that blamed human error for the death of 23 civilians in a drone attack in Afghanistan's Uruzgan province in February.
"While it is by no means perfect, the US military has a relatively public accountability process," he said.
Alston also said that CIA agents could be prosecuted for carrying out drone attacks, because - unlike military personnel - they do not have immunity for their actions.
"CIA personnel could be prosecuted for murder under the domestic law of any country in which they conduct targeted killings, and could also be prosecuted for violations of applicable US law," Alston wrote.
He said the use of drone attacks risked creating a "Playstation" mentality towards killing, "because operators are based thousands of miles away from the battlefield, and undertake operations entirely through computer screens and remote audio-feed".
Drone attacks have been launched mainly in Pakistan's northwestern tribal belt [AFP]
Bill Burton, the White House deputy press secretary, responded to Alston's report by saying that Barack Obama, the US president, was doing "everything that he can to protect Americans [and] to advance our strategic interests".
The CIA's has reportedly carried out more than 150 drone strikes in northwest Pakistan since 2004, resulting in hundreds of casualties.
It is difficult to calculate an exact deathtoll, since many of the targeted areas are off-limits to journalists.
The CIA disputed Alston's conclusions.
"Without discussing or confirming any specific action or programme, this agency's operations unfold within a framework of law and close government oversight. The accountability's real, and it would be wrong for anyone to suggest otherwise," a CIA spokesman said.
Obama has significantly accelerated the drone strike campaign: the CIA has carried out roughly 100 attacks in northwest Pakistan since Obama took office last year.