Al-Awlaki, who is believed to be hiding in Yemen, has become the most notorious English-speaking advocate of terrorism directed at the United States.
E-mails link al-Awlaki to the Army psychiatrist accused of the killings at Fort Hood, Texas, last year. Al-Awlaki has taken on an increasingly operational role in al Qaeda in the Arabian Peninsula, the Justice Department said in a court filing, including preparing Nigerian Umar Farouk Abdulmutallab in his attempt to detonate an explosive device in his underwear aboard a Northwest Airlines flight from Amsterdam to Detroit on Christmas Day 2009.
In its court papers, the Justice Department said that the issues in the case are for the executive branch of government to decide rather than the courts.
The department also said the case entails information that is protected by the military and state secrets privilege.
The courts have sufficient grounds to throw out the lawsuit without resorting to use of the state secrets privilege, the Justice Department said in its filing.
"The idea that courts should have no role whatsoever in determining the criteria by which the executive branch can kill its own citizens is unacceptable in a democracy," the American Civil Liberties Union and the Center for Constitutional Rights said in a statement. "In matters of life and death, no executive should have a blank check."
Al-Awlaki's father, through the CCR and the ACLU, filed the case in federal court in Washington.
"This lawsuit asks for an American court to block the government from protecting its own citizens," Justice Department spokesman Matthew Miller said in a statement.
"It strains credulity to argue that our laws require the government to disclose to an active, operational terrorist any information about how, when and where we fight terrorism," added Miller.
In a declaration filed in federal court, Defense Secretary Robert Gates said he was invoking the military and state secrets privilege on information concerning possible military operations in Yemen, procedures the Defense Department may use in such operations and information concerning Yemen's counterterrorism efforts.
Disclosing information about possible operations would enable targets to evade military action and continue to plot attacks on the U.S., the Gates declaration said.
CIA Director Leon Panetta filed a statement with the court stating that "I am invoking the privilege over any information, if it exists, that would tend to confirm or deny any allegations in the complaint pertaining to the CIA."
Regarding the Christmas bomb attempt, al-Awlaki said in a May 23 interview with the media arm of AQAP that "No one should even ask us about targeting a bunch of Americans who would have been killed in an airplane," James Clapper, the director of national intelligence, said in a declaration accompanying the Justice Department papers.
"Our unsettled account with America includes, at the very least, one million women and children. I'm not even talking about the men," Clapper's declaration quotes al-Awlaki as saying.
The lawsuit filed on the cleric's behalf seeks to have a court declare that the Constitution and international law bar the government from carrying out targeted killings; seeks to block the targeted killing of al-Awlaki; and seeks to force the U.S. government to disclose the standards for determining whether U.S. citizens can be targeted for death.
What al-Awlaki's father is seeking would be "unprecedented, improper, and extraordinarily dangerous," said the Justice Department filing, which neither confirmed nor denied the existence of a targeted killings program.
The lawsuit would necessarily and improperly inject the courts into decisions of the president and his advisers about how to protect the American people from the threat of armed attacks, including imminent threats, posed by a foreign organization against which the political branches have authorized the use of necessary and appropriate force, said the Justice Department filing.
If al-Awlaki were to surrender to the proper authorities, legal principles with which the United States has traditionally and uniformly complied would prohibit using lethal force or other violence against him, the department filing added.
By Associated Press Writer Pete Yost