The National Clandestine Service (NCS) will oversee all human espionage operations - meaning spying by people rather than by technical means.
The chief of the new service will supervise the CIA's espionage operations and co-ordinate all overseas spying, including those of the FBI and the Pentagon.
The director of the new agency, whose identity will remain secret and is simply known as "Jose", will report directly to the head of the CIA, Porter Goss.
"This is another positive step in building an intelligence community that is more unified, co-ordinated and effective," National Intelligence Director John Negroponte said.
Setting up the NCS was one of more than 70 recommendations made by a commission on weapons of mass destruction in March, which was highly critical of the US' intelligence capabilities.
As part of reforms following the 11 September 2001 attacks, the CIA lost overall control of US intelligence to the newly created National Director of Intelligence.