(Adds U.S. government source comment, NSA general counsel, Booz Allen stock close, background on Shadow Brokers probe)
By Julia Edwards and Mark Hosenball
WASHINGTON, Oct 5 (Reuters) - The FBI has arrested a National Security Agency contractor on charges of stealing highly classified information and is investigating possible links to a recent leak of secret hacking tools used to break into the computers of adversaries such as Russia and China, U.S. officials said on Wednesday.
Harold Thomas Martin, 51, was taken into custody in Maryland in August, according to a criminal complaint. A U.S. official, speaking on condition of anonymity, said Martin worked for Booz Allen Hamilton, the consulting firm that employed Edward Snowden when he revealed the vast collection of metadata by the NSA in 2013.
Allegations about a second insider leaking top-secret NSA information could further set back the Obama administration's efforts to recover from Snowden's damaging disclosures about the U.S. government's surveillance and cyber spying activities.
Booz Allen said in a statement that when the company "learned of the arrest of one of its employees by the FBI," they immediately fired him and offered full cooperation to the FBI.
Booz Allen's stock closed down 3.8 percent at $30.31 a share, following the report.
The same month Martin was arrested, some of the NSA's most sophisticated hacking tools were dumped onto public websites by a group calling itself Shadow Brokers.
The U.S. Justice Department charged Martin, who had top secret national security clearance, with theft of classified government material, according to the complaint, which was unsealed on Wednesday. The complaint did not specify Martin's alleged motive, and U.S. officials declined to say.
NSA General Counsel Glenn Gerstell told Reuters that the agency was still assessing damage from the data theft, but said "I don't think this is a Snowden-type situation." Snowden, who has been granted asylum in Russia, has said he deliberately exposed the scope of U.S. government surveillance to force changes.
The New York Times reported that the Federal Bureau of Investigation was looking at whether Martin stole and disclosed highly classified computer "source code" developed to hack into the networks of Russia, China, Iran, North Korea and other countries.
One U.S. government source told Reuters that investigators were not fully convinced that Martin was involved with the Shadow Brokers but another official said the question was still being probed.
It was the latest disclosure of details of cyber spying by the U.S. government since Snowden stole and released a massive trove of documents that exposed the reach of the NSA's surveillance programs at home and abroad.
It also comes at a time of growing concern over the cyberhacking of federal agencies and American political parties.
According to the complaint, documents found in Martin's possession contained sensitive intelligence.
"These six documents were produced through sensitive government sources, methods, and capabilities, which are critical to a wide variety of national security issues," the complaint said. But it did not elaborate.
Martin's lawyer could not immediately be reached for comment.
The Justice Department's chief national security prosecutor, John Carlin, declined to comment on the specifics of the case.
He said, however, that insider threats have long posed a challenge to the government.
"I'm sure the trusted professionals I work with across the community will take a hard look at anything they can learn from this case, whether it's about contractors or other issues to see whether they can better defend our systems from others who might try to steal from them," Carlin said in an interview on CSPAN.
Martin faces up to 10 years in prison if convicted on the most serious charges.
Martin's arrest occurred about two weeks after a leak of classified NSA computer data by the Shadow Brokers.
People with direct knowledge told Reuters in September that a U.S. investigation had focused on a theory that one of its operatives carelessly left them available on a remote computer and Russian hackers found them. Officials in Washington had also floated the possibility that it was the deliberate work of an insider.
The leak of the NSA hacking tools coincided with U.S. officials saying they had concluded that Russia or its proxies were responsible for hacking political party organizations in the run-up to the Nov. 8 presidential election. The Russian government has denied involvement. (Reporting by Dustin Volz, Jim Finkle and Susan Heavey; Writing by Matt Spetalnick; Editing by Andrea Ricci and Lisa Shumaker)