Mark H. Herrington, Associate Deputy General Counsel for the Department of Defense, has written a letter to the American Civil Liberties Union as part of a Freedom of Information Act lawsuit indicating that the Defense Department does not keep separate track of civilian casualties caused by drone strikes.
DoD's search confirmed that DoD does not create or maintain documents to compile estimates of civilian casualties related to drone strikes separately from estimates related to other weapons systems. DoD does possess documents that estimate civilian casualties resulting from operations involving all types of military aircraft. But, as DoD has informed you, generally speaking, weapons fired by drones are treated identically to weapons fired by other aicraft, and these estimates therefore do not differentiate between weapons platforms. The only documents that address estimates of civilian casualties related to drone strikes are individual battle damage assessments evaluating each military aicraft mission, which the ACLU and DoD have agreed are outside the scope of the documents to be processed in this litigation.
Herrington emphasized that the "DoD conducts operations employing measures to avoid or limit civilian casualties as much as possible."
It's important to distinguish between the military's drone program, which is publicly known, and the CIA's drone program, which is publicly known but technically secret. The latter is the one that has caused so much controversy because it involves striking within the borders of Pakistan with the secret permission of that nation's government. I suppose it makes less sense for the military to tabulate civilian casualties separately from those caused by other weapons, since they're not the only airborne weapon they're using that causes civilian deaths, but because of that there's also no way to know if drones tend to kill more noncombatants. The ACLU's Jonathan Manes released a statement criticizing DoD saying, "The public must have accurate information about civilian casualties in drone strikes in order to assess the ethical, legal and strategic concerns that these weapons raise."
The ACLU is seeking information about the CIA program as part of the lawsuit, as well as information about the legal justifications for targeted killings. That's a worthwhile pursuit, although State Department Legal Adviser Harold Koh pretty much explained the rationale in public last year.