US District Court Judge Rosemary M Collyer made the comment at a hearing on a government motion to dismiss the lawsuit. The suit was filed by relatives of the three men killed in the drone strikes, charging that the attacks violated the Constitution.
It named as defendants then-Defense Secretary Leon Panetta, then-CIA Director David Petraeus and two commanders in the military's Special Operations forces, and seeks unspecified compensatory damages.
US-born al-Qaeda leader Anwar al-Awlaki and Samir Khan, an al-Qaeda propagandist, were killed in a drone strike in September 2011. Al-Awlaki's 16-year-old son, Abdulrahman, was killed the following month.
Al-Awlaki had been linked to the planning and execution of several attacks targeting US and Western interests, including a 2009 attempt on the Detroit-bound airliner and a 2010 plot against cargo planes.
The government has argued that the matter is best left to Congress and the executive branch, not judges, and that courts have recognised that the defence of the nation is best left to those political branches.
When Hauck mentioned the constitutional structure as one such constraint, Collyer replied that the US Constitution sets out three branches of government, including the judiciary "the one that's usually yelled at and not given any money."
She added: "I consider us a nation of laws, and everybody from the president down to homeless people have to follow the law."
"Where was the due process in this case?" asked Collyer, an appointee of President George W Bush. Hauck said there were checks in place, including reviews done by the executive branch.
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