Both the FBI and CIA are calling it the first case of espionage in the White House in modern history.
Officials tell ABC News the alleged spy worked undetected at the White House for almost three years. Leandro Aragoncillo, 46, was a U.S. Marine most recently assigned to the staff of Vice President Dick Cheney.
"I don't know of a case where the vetting broke down before and resulted in a spy being in the White House," said Richard Clarke, a former White House advisor who is now an ABC News consultant.
Federal investigators say Aragoncillo, a naturalized citizen from the Philippines, used his top secret clearance to steal classified intelligence documents from White House computers.
In 2000, Aragoncillo worked on the staff of then-Vice President Al Gore. When interviewed by Philippine television, he remarked how valued Philippine employees were at the White House.
"I think what they like most is our integrity and loyalty," Aragoncillo said.
Officials say the classified material, which Aragoncillo stole from the vice president's office, included damaging dossiers on the president of the Philippines. He then passed those on to opposition politicians planning a coup in the Pacific nation.
"Even though it's not for the Russians or some other government, the fact that it occurred at the White House is a matter of great concern," said John Martin, who was the government's lead espionage prosecutor for 26 years.
Last year, after leaving the Marines, Aragoncillo was caught by the FBI while he worked for the Bureau at an intelligence center at Fort Monmouth, N.J.
According to a criminal complaint, Aragoncillo was arrested last month and accused of downloading more than 100 classified documents from FBI computers.
"The information was transferred mostly by e-mails," said U.S. Attorney Christopher J. Christie at the time of Aragoncillo's arrest.
Since that arrest, officials say Aragoncillo has started to cooperate. He has admitted to spying while working on the staff of Vice President Cheney's office.
Aragoncillo began working at the White House in 1999. Officials are now trying to learn how he landed the job, when he started spying, and how he escaped detection for so long.
"Of course, it is a source of embarrassment when you find out that this kind of activity has been carried out literally right under your nose," said Martin, the former espionage prosecutor.
According to friends, in addition to his work for Cheney and Gore, Aragoncillo claimed he also worked with President Clinton and Condoleezza Rice when she was the national security advisor.
ABC News' Vic Walter, Avni Patel and Rhonda Schwartz contributed to this report.