Among the agencies are the Malaysian Anti-Corruption Commission (MACC), the Election Commission (EC), the Human Rights Commission of Malaysia (Suhakam), the Public Prosecutor's Office and the National Audit Department.
This is just part of the massive overhaul of the Prime Minister's Department.
The Public Service Commission, Education Service Commission and the Judicial Appointments Commission will also report directly to Parliament, which will be an independent entity.
In a June 26 letter addressed to the Prime Minister's Department sighted by The Star, Chief Secretary to the Government Tan Sri Dr Ali Hamsa approved the abolition of 10 departments and agencies including 19 other smaller divisions or offices under the Prime Minister's Office.
It also includes the merging of five agencies and the redesignation of 40 agencies.
The country's special envoy on Infrastructure to India and South Asia Tun S. Samy Vellu will have his services terminated after his contract expires at the end of the year.
The special envoy post is with ministerial rank.
The office, including that of the Special Envoy to China, will also be abolished. Tan Sri Ong Ka Ting had relinquished his post as the special envoy in January.
Tan Sri Dr Rais Yatim, who was the Socio-Cultural Advisor to the Government, also had his services ended on Saturday (June 30), along with the expiry of his contract.
As expected, the Land Public Transport Commission (SPAD) has been abolished and its functions absorbed by the Transport Ministry.
Others abolished included the National Professors Council, the National Innovation Agency, the Special Implementation Task Force, Civil Service Delivery Unit (CSDU) and the 2050 National Transformation (TN50) secretariat.
Meanwhile, the Attorney General's Chambers is still under the Prime Minister's Department but its prosecuting functions have been placed under the Public Prosecutor's Office.
The Legal Aid Department and Insolvency Department will also be merged with the Law and Judiciary Ministry.