Being the country that contains the largest Muslim population in the world, Islamic principles do play an important role in the nation's political decision making, but Indonesia is not a Muslim or Islamic state.

Political decentralization in the post-Suharto era has brought more power to the regional governments and this development implied that regional decision-making has become more affected by the regional religious context. In strict Muslim areas, implemented policies can include the regional banning of pork businesses or the obligation for women to wear the headscarf, while in Christian regions (located mostly in eastern Indonesia) such policies seem impossible to be implemented.

However, given the nation's clear Muslim majority and the dominance of (Muslim) Java in national politics, Indonesia - as a whole - is far more Islam oriented. To have a president that is non-Muslim, therefore, seems impossible. On the other hand, Indonesian Islam can generally be labelled 'moderate' as the majority of Indonesian Muslims consist of nominal Muslims. For example, the majority of the Indonesian Muslim community will not agree with the implementation of Islamic law (Sharia). Another example is that when Megawati Soekarnoputri became the first female Indonesian president in 2001, only a small minority rejected her based on certain Islamic doctrine that women cannot take leading positions.

The Indonesian political system consists of three branches:

Executive branch
Legislative branch
Judicial branch

Executive branch of Indonesia

The executive branch consists of the president, the vice president and the cabinet. Both the president and vice president are chosen by the Indonesian electorate through presidential elections. They serve for a term of five years that can be extended once by another term of five years when re-elected by the people. During these elections the president and vice president run as a fixed, inseparable pair, which implies that the composition of this pair is of great political strategic importance. Important matters that are of influence include ethnic (and religious) background and (previous) social position in Indonesian society.

In terms of ethnicity and religion, a Javanese Muslim will enjoy more popular support as the majority of the Indonesian people consist of Javanese Muslims. In lower political positions (and depending on the regional religious context) political leaders that are non-Muslim are possible (for example, the current Governor of Jakarta is Chinese-Christian Basuki Cahaya Purnama).

With regard to (previous) social position in society there are a few categories that all enjoy popular support from part of the people. These categories include (retired) army generals, businessmen, technocrats and leading Muslim scholars. Therefore, to optimize chances of winning the election the president and vice president usually come from different social categories in order to grasp a larger share of the popular vote. For example, former president Yudhoyono (himself a retired army general and a Muslim) chose Boediono (a Javanese Muslim technocrat) as vice president in his presidential campaign of 2009. As Boediono is an experienced economist, it raised people's trust in the pair. Despite Indonesia's authoritarian past under Suharto, army generals who run for president can still count on much popular support in present Indonesia as they are considered being strong leaders.

Meanwhile, current president Joko Widodo (a Javanese Muslim and former businessman) chose to pair with Jusuf Kalla (a businessman, politician and Muslim from Sulawesi). Kalla has a long history in Indonesian politics (particularly in the Golkar party, Suharto's old political vehicle) and enjoys widespread popularity in Indonesia (especially outside the island of Java). Widodo was basically a newcomer to national politics at the start of 2014 but Kalla's long-standing experience in politics gave the pair more political credibility.

After election, the new president appoints a cabinet that usually consists of members from his own party, the coalition partners and non-partisan technocrats. To see Indonesia's current cabinet composition, go here.

Legislative branch of Indonesia

Indonesia's legislative branch is the People’s Consultative Assembly (Majelis Permusyawaratan Rakyat, abbreviated MPR). It has the power to set or change the Constitution and appoints (or impeaches) the president. The MPR is a bicameral parliament that consists of the People’s Representative Council (Dewan Perwakilan Rakyat, abbreviated DPR) and the Regional Representative Council (Dewan Perwakilan Daerah, abbreviated DPD).

The DPR, consisting of 560 members, draws up and passes laws, produces the annual budget in cooperation with the president and oversees the general performance of political affairs. It is elected for a five-year term through proportional representation based on general elections. Remarkably, this DPR is notorious due to the frequent occurrences of corruption scandals among its members.

The DPD deals with bills, laws and matters that are related to the regions, thus increasing regional representation at the national level. Every Indonesian province elects four members to the DPD (who serve for a five-year term) on non-partisan basis. As Indonesia contains 33 provinces, the DPD consists of a total of 132 members.

Judicial branch of Indonesia

The highest court in Indonesia's judiciary system is the independent Supreme Court (Mahkamah Agung). It is the final court of appeal and also deals with disputes between lower courts. A relatively new court, established in 2003, is the Constitutional Court (Mahkamah Konstitusi), which monitors whether decisions made by the cabinet and parliament (MPR) are in line with the Indonesian Constitution. However, most of the legal cases in Indonesia are handled by the public courts, administrative courts, religious courts and military courts.

A Judicial Commission (Komisi Yudisial) oversees the maintenance of honour, dignity and behaviour of Indonesian judges. There are frequent reports claiming that Indonesia's judiciary institutions are not free from corruption and are not fully independent from the other political branches.