After the collapse of the Second Ali Sastroamidjojo Cabinet in 1957, Leimena took a position where he stated that further collapses of cabinets could only be prevented by a more inclusive government, including political parties and groups previously excluded.
Within the Djuanda Cabinet which started on 9 April 1957, Leimena was initially appointed as Social Minister, but by that year as well he was relieved from that post and instead became a Deputy Prime Minister.
Leimena joined the "National Council" which was formed in May 1957, and late in 1957, Leimena was also appointed into a "Committee of Seven" intended to manage undergoing issues with the Indonesian Army.
Other members of the committee were Sukarno, Mohammad Hatta, Djuanda Kartawidjaja, Abdul Haris Nasution, Hamengkubuwono IX, and Azis Saleh.
Leimena was a loyalist of Sukarno, including after Sukarno's 1959 Decree.
During 1957–1959, he largely passed over the work of being Parkindo chairman to A.M. Tambunan.

After the 1959 Decree, Leimena was appointed Distribution Minister, and shortly afterwards also became Deputy First Minister.
Within his capacity as Distribution Minister, he saw nutritional intake as vital in improving worker productivity and desired to achieve rice self-sufficiency for the growing population through intensification of rice cultivation in Java while expanding farmlands elsewhere.
Despite his ambitious plans, coordination with the Ministries of Agriculture, Transmigration and Labor proved an issue.

Leimena was part of the Supreme Operations Command (Komando Operasi Tertinggi/KOTI) in 1962 during the West New Guinea dispute.
He was given a titular rank of a vice admiral of the Indonesian Navy in 1962, and was promoted to admiral on 17 August 1964.
In November 1963, following the unexpected death of Djuanda, a presidium was appointed by Sukarno to manage the cabinet, consisting of Leimena, Subandrio, and Chaerul Saleh.
During the whole of the Guided Democracy period, Leimena remained a close ally of Sukarno, being skilled with handling the political elite, though he lacked the ability to organize large-scale popular support.
Due to his position as Deputy First Minister, he took over presidential duties as acting president seven times on occasions.
After the collapse of the Second Ali Sastroamidjojo Cabinet in 1957, Leimena took a position where he stated that further collapses of cabinets could only be prevented by a more inclusive government, including political parties and groups previously excluded. Within the Djuanda Cabinet which started on 9 April 1957, Leimena was initially appointed as Social Minister, but by that year as well he was relieved from that post and instead became a Deputy Prime Minister. Leimena joined the "National Council" which was formed in May 1957, and late in 1957, Leimena was also appointed into a "Committee of Seven" intended to manage undergoing issues with the Indonesian Army. Other members of the committee were Sukarno, Mohammad Hatta, Djuanda Kartawidjaja, Abdul Haris Nasution, Hamengkubuwono IX, and Azis Saleh. Leimena was a loyalist of Sukarno, including after Sukarno's 1959 Decree. During 1957–1959, he largely passed over the work of being Parkindo chairman to A.M. Tambunan.
After the 1959 Decree, Leimena was appointed Distribution Minister, and shortly afterwards also became Deputy First Minister. Within his capacity as Distribution Minister, he saw nutritional intake as vital in improving worker productivity and desired to achieve rice self-sufficiency for the growing population through intensification of rice cultivation in Java while expanding farmlands elsewhere. Despite his ambitious plans, coordination with the Ministries of Agriculture, Transmigration and Labor proved an issue.
Leimena was part of the Supreme Operations Command (Komando Operasi Tertinggi/KOTI) in 1962 during the West New Guinea dispute. He was given a titular rank of a vice admiral of the Indonesian Navy in 1962, and was promoted to admiral on 17 August 1964. In November 1963, following the unexpected death of Djuanda, a presidium was appointed by Sukarno to manage the cabinet, consisting of Leimena, Subandrio, and Chaerul Saleh. During the whole of the Guided Democracy period, Leimena remained a close ally of Sukarno, being skilled with handling the political elite, though he lacked the ability to organize large-scale popular support. Due to his position as Deputy First Minister, he took over presidential duties as acting president seven times on occasions.
Johannes Leimena