Executive Secretary Eduardo Ermita and Presidential Chief of Staff Michael Defensor said the appointment was made last week.
The controversial Berroya, a former Philippine National Police (PNP) director, replaces Annelli Lontoc, who was promoted to transportation undersecretary last month.
Prior to his appointment to the top LTO post, Berroya was the head of the LTO in the National Capital Region.
At the PNP, he served as intelligence chief and head of the police command in Southern Tagalog.
Berroya belongs to the Philippine Military Academy (PMA) Class 1968 and was a classmate of Transportation and Communications Secretary Leandro Mendoza, who once headed the PNP.
Mendoza and Berroya played a crucial role in the protection of Mrs. Arroyo at the time the vice president in the weeks leading up to EDSA 2, the popular uprising in January 2001 that led to the ouster of Joseph Estrada from the presidency.
Berroya, along with former Constabulary colonel Billy Bibit and police director Eduardo Matillano, worked discreetly with anti-Estrada forces.
Once a close ally of then Vice President Estrada, Berroya once headed the Anti-Kidnapping Task Force Habagat, a police anti-kidnapping unit that got
entangled with an anti-kidnapping police unit headed by Senior Superintendent and now Sen. Panfilo Lacson. Task Force Habagat was also then under Estrada.
Estrada and Berroya were drinking buddies before their falling out that ended in his (Berroyas) conviction and incarceration at the New Bilibid
Prisons in Muntinlupa for the Chou Chueng Yih alias Jack Chous kidnapping in May 11, 1993.
Cleared later by the courts, Berroya was reinstated to the police service.
But during Estrada administration, he was placed on floating status. Immediately after EDSA 2, Berroya was assigned to various police positions, retiring later with a one-year extension of service, as director of the Philippine National Police-Civil Security Group (CSG).
A Bulakeno, Berroya is married to environmentalist Inday Berroya and is the father of two daughters, Liza, a former beauty queen, and Baia.
His appointment is the latest of Mrs. Arroyos revamp of her official family in the past weeks.
She appointed on Oct. 25 members to the Movie and Television Review and Classification Board (MTRCB) Appeals Committee that she revived under Executive Order 572.
Ermita said the new set of officers of the MTRCB appeals body are Cecile Guidote-Alvarez, representing the Office of the President; Undersecretary Roberto Rivera of the Office of the Press Secretary (OPS) as vice chairman, representing the OPS.
Also named to the MTRCB appeals committee were Roesholm Camaligan, representing the movie industry; Rodolfo Lacuna, TV Industry, and Michael Francis Lopez, Youth Commission.
He said the President also elevated the appointment of acting Land Bank president and chief executive officer (CEO) Gilda Elepano-Pico to president and CEO.
Ermita stressed the reshuffling of Cabinet members is normal and it is the Presidents prerogative to remove, appoint or transfer officials as she sees fit.
"A Cabinet reshuffle is considered a normal activity in bureaucracy and the President alone determines that at certain times when she feels it would enhance the implementation of certain projects," Ermita told reporters last week.
Mrs. Arroyo also appointed last month Presidential Management Staff (PMS) Director General Arthur Yap as agriculture secretary to replace Domingo Panganiban, who in turn will chair the National Anti-Poverty Commission (NAPC).
The NAPC is headed by Secretary Cerge Remonde, who concurrently heads the Government Mass Media Group. Remonde will take over Yaps PMS post.
The President also transferred Land Transportation Franchising Regulatory Board chairman Ma. Elena Bautista to the DOTC as undersecretary. She was replaced by DOTC spokesman Thompson Lantion.
Ermita also announced on Wednesday the appointments of Cesar Sarmiento and Elmer Soneja both as acting assistant secretaries of the DOTC.
Also appointed by the President were Benedicto Ernesto Bitonio as senior vice president of the Development Bank of the Philippines, Gerardo Benjamin Nograles as acting chairman of the National Labor Relations Commission.
Mrs. Arroyo also promoted Press Assistant Secretary Martin Crisostomo to become undersecretary under the Office of the President to handle media affairs. With Jaime Laude