He argues that conventional military forces are more accountable than intelligence agencies for investigating civilian casualties.
"With the defence department you've got maybe not perfect but quite abundant accountability as demonstrated by what happens when a bombing goes wrong in Afghanistan," Alston said.
"The whole process that follows is very open. Whereas if the CIA is doing it, by definition they are not going to answer questions, not provide any information, and not do any follow-up that we know about."
Under international law, soldiers representing conventional militaries are allowed to kill enemy troops in war zones.
The government of George Bush, the previous US president, issued a policy manual in 2007 which defined "murder in violation of the laws of war" as killing someone who did not meet "the requirements for lawful combatancy".
These requirements include being part of a regular army or otherwise wearing a uniform.
According to this definition of murder, CIA drone operators, who do not wear the uniforms of conventional soldiers, could theoretically be considered war criminals and subject to prosecution in Pakistani courts.
Paul Weiss, a CIA spokeswoman, said that the "agency's operations take place in a framework of both law and government oversite".
"It would be wrong to suggest the CIA is not accountable," he said, although she refused to discuss or confirm specific activities.
By some accounts, drone attacks - which reportedly commence at CIA headquarters in Langley, Virginia - have increased during president Barack Obama's time in office.
The Long War Journal, a blog that uses open-source information to track US operations in the Middle East, tallied five US aerial attacks in Pakistan in 2007 and 36 in 2008.
In 2009, Obama's first year in office, aerial attacks increased 47 per cent to 53, with unmanned drones responsible for most strikes.