Aswismarmo, an Indonesian scholar and historian, noted that BRIN is a form of "holding research institution".

The decree is intended to outline the national research policies and priorities for comprehensive sustainable development.

[12] Bambang Brodjonegoro, the Minister of Research and Technology, failed to set the structure of BRIN by the deadline; a further temporary extension was issued, to 30 April 2020.

The People's Representative Council requested Joko Widodo to warn the ministries to work together and consolidate their efforts.

The executive, which oversees research and day-to-day activities, as directed by the steering committee, is headed by the chairman.

[25] On 20 September 2021, it was revealed that more than 11,000 employees of the former Ministry of Research and Technology, LIPI, BPPT, LAPAN, and BATAN were being moved from their original institutions to BRIN.

[28] To strengthen BRIN's ability to coordinate all national research with those at the regional and local levels, on 22 July 2021 the Ministry of State Apparatus Utilization and Bureaucratic Reform issued Circular No.

The issues were: (1) the transfer of human resource from the institutions that were to be subsumed into BRIN, and (2) the difficulties involved in the formation of BRIDA.

[31][32][33] On 28 August 2021, BRIN, announced plans to cut off and dismantle redundant state research institutions and centers of excellence (COEs) in Indonesia to achieve efficiency in funding.

BRIN also developed means to prevent the formation of such institutions in the future, to avoid redundant and needlessly costly research efforts.

[38] Two researchers, Eko Noer Kristianto and Heru Susetyo, submitted a judicial review to the Constitutional Court to challenge the government decision.

The announcement outlined 5 major points of revision: (1) Changes to the presidential decree's articles that conflicted with preexisting laws; (2) Clarification of the integration mechanisms; (3) Harmonization between BRIN and other scientific and scientific regulatory agencies; (4) Fixing inter-agency coordination issues; (5) Setting up 10 to 11 Technical Implementing Organizations under BRIN.

Despite that, the said revision planned to clarify the differences between BRIN and the Ministry of Education, Culture, Research and Technology in regulating science in Indonesia.

For example, LAPAN would become the Aeronautics and Space Research Organization (Organisasi Riset Penerbangan dan Antariksa (ORPA)).

The logo was drawn by Triawan Munaf [id], former chief of the Creative Economy Agency of Jokowi's previous Working Cabinet.

The decree officially gave BRIN the power and status of a ministerial office, as a cabinet-level agency (termed as Lembaga Setingkat Kementerian).

With their inauguration, LIPI, BPPT, LAPAN, and BATAN come to the end, but their integration process still continued, with its expected completion pushed back to one year after the enactment of Decree No.78/2021.

[62] On 13 October 2021, after a period of controversy since May 2021, Megawati Soekarnoputri, Sri Mulyani, Suharso Monoarfa, Sudhamek Agung Waspodo Sunyoto, Emil Salim, I Gede Wenten, Bambang Kesowo, Adi Utarini, Marsudi Wahyu Kisworo, and Tri Mumpuni were inaugurated as BRIN Steering Committee members by President Widodo.

[63][64][65] In an attempt to consolidate state research activities under BRIN, the Indonesian government changed several ministries affected by the reform.

[82][83] While it was desired by Indonesia's scientific community, the formation of BRIN was criticized due to its being coordinated with and sharing the same Steering Committee with BPIP.

Critics are afraid that in doing so, BRIN becomes politicized and vulnerable to government intervention, which would threaten scientific freedom.

This controversy arose largely because Megawati, a member of the BRIN steering committee, is also a political party leader.

[84] The opposition Prosperous Justice Party also lamented the decision, because the Steering Committee office was not mandated by Bill No.

Azyumardi Azra, an Indonesian Islamic scholar, lamented the agency's merging strategy that was expected to take place over a very short period of time.

[94] Not only that, with the status of only research and development agency, not a group of ministries as before, the bargaining power of BRIN would be weak.

[56] Not only the formation of BRIN, the formation of BRIDA offices across Indonesia was also difficult, largely because regional and local research and development agencies had been so long neglected, lacking resources, with their researches limited by regional and local policy making and lack of innovation.

[1][97] Endang S. Thohari, former Ministry of Agriculture scientist, and one of the founders of Balitbangtan, who is currently a Great Indonesia Movement Party (Gerindra) politician sitting on Commission IV, also lamented the government's decision to liquidate the agency she founded with Indonesian agricultural scientists.

The PKS had made numerous attacks, called "criticisms", against the new institution since the beginning of the separation of BRIN from the Ministry of Research and technology.

The Islamist party also used an Islamic-themed populist narrative in an attempt to delegitimize BRIN's existence and claimed that BRIN's existence was part of a "de-Habibie-nization project", accusing the Widodo administration of attempts to "remove landmarks left by Habibie and other Islamic scholars and scientists in building Indonesia research ecosystem" and favoring a "secular model of scientific development" rather than a religious one.

[111] One Commission VII DPR member, Syaikhul Islam Ali from the National Awakening Party, even asked that Laksana replacement not necessarily be a researcher, but a manager with the capability to be a chairman of BRIN.