"On drone strikes, our position has been very clear... there are humanitarian aspects, there are sovereignty and legal issues which are also a subject of debate," Foreign Secretary Jalil Abbas Jilani told a news conference.
"We have a position on drone attacks that we have articulated from time to time, we have made it clear during our discussions with our American interlocutors," he said in response to questions about Obama's new guidelines for drone strikes.
"We have been saying this all along and we have been saying we should develop a strategy which addresses the root causes of the problem that we are confronted with," he said.
The Pakistan government has noted the changes in US counter-terrorism policy outlined yesterday by Obama during his speech in Washington, Jilani said.
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He welcomed the "positive elements" of the speech, including the acknowledgement of the sacrifices by Pakistani forces while fighting terrorism.
A statement issued earlier in the day by the Foreign Office said the Pakistan government had "consistently maintained that drone strikes are counter-productive, entail loss of innocent civilian lives, have human rights and humanitarian implications and violate the principles of national sovereignty, territorial integrity and international law".
Obama mounted a strong defence of the covert drone war as legal and just but warned that undisciplined use of the spy planes would invite charges of abuse of power.
He said he had approved new guidelines stating that drone strikes can only be used to prevent imminent attacks and when the capture of a suspect is not feasible and if there is a "near certainty" that civilians won't be killed.