The USC's announcement of a provisional government in February 1991 angered its allies, who maintained that they had not been consulted. Other opposition movements, particularly the SSDF, felt that the USC had slighted their long years of struggle against the Siad Barre regime, and refused to accept the legitimacy of the provisional government. The SPM and the SSDF formed a loose alliance to contest USC control of the central government and ousted USC forces from Chisimayu, Somalia's main southern city. Violent clashes throughout March threatened to return the country to civil war. Although in early April 1991, the USC and its guerrilla opponents in the south agreed to a cease-fire, this agreement broke down in the latter part of the year as fighting spread throughout those areas of Somalia under the nominal control of the the provisional government. The provisional government was continuing to hold talks on power sharing, but the prospects for long-term political stability remained uncertain.

The situation in northern Somalia was even more serious for the provisional government. The dominant SNM, whose fighters had evicted Siad Barre's forces from almost all of Woqooyi Galbeed, Togdheer, and Sanaag regions as early as October 1990, had also captured the besieged garrisons at Berbera, Burao, and Hargeysa at the end of January they were not prepared to hand over control to the new government in Mogadishu. Like its counterparts in the south, the SNM criticized the USC's unilateral takeover of the central government, and the SNM leadership refused to participate in USC-proposed unity talks. The SNM moved to consolidate its own position by assuming responsibility for all aspects of local administration in the north. Lacking the cooperation of the SNM, the provisional government was powerless to assert its own authority in the region. The SNM's political objectives began to clarify by the end of February 1991, when the organization held a conference at which the feasibility of revoking the 1960 act of union was seriously debated.

In the weeks following Siad Barre's overthrow, the SNM considered its relations with the non-Isaaq clans of the north to be more problematic than its relations with the provisional government. The SDA, supported primarily by the Gadabursi clan, and the relatively new United Somali Front (USF), formed by members of the Iise clan, felt apprehension at the prospect of SNM control of their areas. During February there were clashes between SNM and USF fighters in Saylac and its environs. The militarily dominant SNM, although making clear that it would not tolerate armed opposition to its rule, demonstrated flexibility in working out local power-sharing arrangements with the various clans. SNM leaders sponsored public meetings throughout the north, using the common northern resentment against the southernbased central government to help defuse interclan animosities. The SNM administration persuaded the leaders of all the north's major clans to attend a conference at Burao in April 1991, at which the region's political future was debated. Delegates to 8f9 o the Burao conference passed several resolutions pertaining to the future independence of the north from the south and created a standing committee, carefully balanced in terms of clan representation, to draft a constitution. The delegates also called for the formation of an interim government to rule the north until multiparty elections could be held.

The Central Committee of the SNM adopted most of the resolutions of the Burao conference as party policy. Although some SNM leaders opposed secession, the Central Committee moved forward with plans for an independent state, and on May 17, 1991, announced the formation of the Republic of Somaliland. The new state's border roughly paralleled those of the former colony, British Somaliland. SNM Secretary General Abdirahmaan Ahmad Ali "Tour" was named president and Hasan Iise Jaama vice president. Ali "Tour" appointed a seventeen-member cabinet to administer the state. The SNM termed the new regime an interim government having a mandate to rule pending elections scheduled for 1993. During 1991 and 1992, the interim government established the sharia as the principal law of the new republic and chose a national flag. It promised to protect an array of liberties, including freedom of the press, free elections, and the right to form political parties, and tried, albeit unsuccessfully, to win international recognition for the Republic of Somaliland as a separate country.