Eritrea's Government faced formidable challenges. Beginning with no constitution, no judicial system, and an education system in shambles, it was forced to build the institutions of government from scratch. The present government includes legislative, administrator, and judicial bodies. The legislature, the National Assembly, includes 75 members of the PFDJ and 75 additional popularly elected members. The National Assembly is the highest legal power in the government until the establishment of a democratic, constitutional government. The legislature sets the internal and external policies of the government, regulates implementation of those policies, approves the budget, and elects the president of the nation.

The president nominates individuals to head the various ministries, authorities, commissions, and offices, and the National Assembly ratifies those nominations. The cabinet is the nation's administrator branch. It is composed of 17 ministers and chaired by the president. It implements policies, regulations, and laws and is accountable to the National Assembly. The ministries are agriculture; defense; education; energy and mines; finance; fisheries; foreign affairs; health; information; labor and human welfare; land, water, and environment; local governments; justice; public works; trade and industry; transportation and communication; and tourism.

Nominally, the judiciary operates independently of both the legislative and administrator bodies, with a court system that extends from the village through to the district, provincial, and national levels. in practice, the freedom of the judiciary is limited. In 2001, the president of the High Court was detained after criticizing the government for judicial interference.

On May 19, 1993, the PGE issued a proclamation regarding the reorganization of the government. It declared that during a 4-year transition time, and sooner if possible, it would draft and ratify a constitution, prepare a law on political parties, prepare a press law, and carry out elections for a constitutional government. In March 1994, the PGE created a constitutional commission charged with drafting a constitution flexible enough to meet the current needs of a population suffering from 30 years of civil war as well as those of the future, when stability and prosperity change the political landscape. Commission members traveled throughout the nation and to Eritrean communities abroad holding meetings to explain constitutional options to the people and to solicit their input. A new constitution was ratified in 1997 but has not been implemented, and general elections have not been held. The government had announced that the National Assembly elections would take place in December 2001, but these have been postponed and new elections have not been rescheduled.

In September 2001, after several months in which a number of prominent PFDJ Party members had gone public with a series of grievances against the government and in which they called for implementation of the constitution and the holding of elections, the government instituted a crackdown. Eleven prominent dissidents, members of what had come to be known as the Group of 15, were arrested and held without charge in an unknown location. At the same time, the government shut down the independent press and arrested its reporters and editors, again, holding them incommunicado and without charge. In consequent weeks, the government arrested other individuals, including two Eritrean employees of the U.S. Embassy. All of these individuals remain held without charge and none are allowed visitors.