This article aims to explain how the government system and the history of the administration of the State of East Indonesia from 1946-1950. The method used in this study is a historical method with data collection techniques using library research. The State of East Indonesia (NIT) was formed through two negotiations, namely the Malino Negotiation and the Denpasar Conference in 1946. The system of government of the State of East Indonesia is held by the president, prime minister, and chairman of the parliament, while regional government is led by the king. The beginning of the NIT administration was passed with instability, political turmoil, and tenuous relations with the Republic of Indonesia. However, during the reign of the prime minister Anak Agung things changed and NIT was able to improve relations with RI and help RI to gain its sovereignty. In 1949, NIT merged into the state of the Republic of the United States of Indonesia (RIS). After becoming part of the RIS state, there was a mass movement in NIT and demonstrators asked for NIT to be disbanded and reintegrated into RI. There was resistance by Chris Soumokil and Andi Azis to stop the process of integrating NIT into RI by carrying out a rebellion. However, their efforts failed and in April 1950, NIT began preparations to rejoin RI. Finally, the State of East Indonesia was officially dissolved on 17 August 1950 when President Soekarno dissolved the RIS.