By David Ingram

WASHINGTON (Reuters) - A U.S. appeals court responded skeptically on Thursday to Obama administration assertions the government can withhold documents about a program that uses aerial drones for targeted killings overseas.

A suit brought by the American Civil Liberties Union is part of a broad legal strategy, also playing out in federal court in New York, to learn more about the drone program that the government says targets al Qaeda militants.

The program is shrouded in secrecy, even as officials up to President Barack Obama acknowledge it exists.

What remains in dispute is whether the government has confirmed the involvement of the CIA in the program, and if so, whether the CIA must turn over documents to the ACLU.

Pressing government lawyer Stuart Delery, Judge Merrick Garland asked, "If the CIA is the emperor, aren't you asking us to say that the emperor has clothes even when the emperor's bosses say it doesn't?"

All three appeals judges read aloud to a full courtroom statements from U.S. officials, some of them anonymous, that the judges said made the government's case difficult.

A 2010 story in The Washington Post about drone attacks quoted Leon Panetta, then the CIA director, describing "the most aggressive operation that CIA has been involved in our history."

After Judge David Tatel asked Delery about the passage, Delery responded that Panetta was "talking about CIA efforts generally, but not any specific technique."

Given the high stakes of the operations, Delery told the appeals judges that they should have a "very high bar" before finding that the CIA had disclosed its involvement.

DOCUMENTS AT STAKE

A ruling against the government could lead to the release of such information as the government's legal explanation of how the targeted killings comply with international law and the rights of U.S. citizens abroad.

A drone strike in Yemen in September 2011 killed Anwar al-Awlaki, a U.S.-born Muslim cleric who joined al Qaeda's Yemen affiliate, and naturalized U.S. citizen Samir Khan.

Any decisions to force the release of documents would be made by a lower court in what could be a lengthy process.

U.S. officials call the drone strikes an essential element of their attacks on al Qaeda militants and their affiliates in countries such as Pakistan and Yemen, even as those strikes ignite local anger and fray diplomatic relations.

Attacks on people born in the United States or having U.S. citizenship have received widespread attention, and U.S. officials have spoken, often anonymously, to media outlets about them and about other drone attacks.

Judge Thomas Griffith asked whether an anonymous statement to the media - what the ACLU calls a pattern of strategic leaks - "in facts works as an acknowledgement." Could outlets such as The New York Times be misinformed, he asked?

Delery urged the court not to turn a case about documents into a case about leaks, and said government officials must feel free to speak with the press.

FOCUS ON PANETTA

ACLU lawyer Jameel Jaffer faced friendlier questions.

Garland told Jaffer that the lawyer had stronger arguments than he was using. "You have the president of the United States announcing, 'We have a drone program.' If I were you, I'd start with that," Garland said.

Panetta, now the U.S. defense secretary, was a particular focus as the judges and Jaffer returned multiple times to speeches and interviews he gave.

In May 2009, while Panetta was CIA director, he gave a speech in which an audience member asked about drone strikes. He responded, "These operations have been very effective because they have been very precise in terms of the targeting and it involved a minimum of collateral damage."

That statement "discloses that the CIA has a drone program that is engaged in targeted killing," or at least has documents related to a broader program, Jaffer said.

The case is American Civil Liberties Union v. Central Intelligence Agency, U.S. Court of Appeals for the District of Columbia Circuit, No. 11-5320.

(Reporting by David Ingram; Editing by Howard Goller and Vicki Allen)