General Samih Asfura replaces Saad Khair, who was promoted to field marshal, Petra said.
It said Asfura's appointment was effective immediately as dictated in a royal decree issued by the king, who holds the title of supreme commander of the Jordanian armed forces.
The change comes a month after a new cabinet was sworn in as part of a wide-ranging reshuffle in top government posts.
Abdullah instructed Khair - who served as intelligence chief since November 2000 - to keep his post as a security adviser, a top position in Jordan's security apparatus.
The king offered no explanation about the duties of the planned National Security Agency, but it was believed that it will serve as a coordination body between all Jordanian security departments, including police.
Asfura, in his 50s, held top positions in Jordan's largely feared General Intelligence Department for at least two decades, including director of administration and later an assistant to Khair. He is known to be a soft-spoken professional with extensive operational experience.
Asfura served as head of a special military court, which found former intelligence chief Samih Batikhi guilty of fraud and embezzlement in a case involving shady loans to businessmen. In July 2003, Batikhi was sentenced to four years in jail.
Asfura and Khair served as Batikhi's assistants in the late 1990s.