Yusuf early this week arrived in Jowhar, some 90 km north of Mogadishu, to launch the establishment of the first presidential office on Somali soil for more than a decade.
The president flew from his personal stronghold in the northern region of Puntland to the town of Jowhar, where he believes his personal safety and popularity is more secure.
"The president is expected to continue implementing his political program in Jowhar where he will stay for many days," Presidential Spokesman Yusuf Mohammed Ismail said.
President Yusuf, however, has refused to move to Mogadishu, the capital where he has almost no support among the civilian population and among the armed groups still controlling the city.
Some ministers, including Prime Minister Ali Mohamed Gedi, have chosen to follow President Yusuf to Jowhar and he has been operating there since June 18.
Somalia has been without a stable government since clan-based warlords overthrew dictator Mohamed Siad Barre in 1991. The warlords then turned on each other, plunging the Horn of Africa country into chaos.
Last year Somalia's parliament and government were formed after two years of peace talks, but they were based in Kenya because Somalia was considered too dangerous.
The Mogadishu-based warlords, clans and armed groups traditionally have been in strong opposition to groups from the north and President Yusuf holds that his safety cannot be assured in the capital.
The split became apparent in May as President Yusuf fell out with Parliament Speaker Sheriff Hassan Sheikh Aden and other officials such as Home Security Minister Mohammed Qanyare Affrah, who has set up operations in Mogadishu, together with more than 100 legislators and some Cabinet members.
Sheikh Adan and warlords, also ministers in the federal government, insisted that Mogadishu would remain capital of Somalia at any cost as stipulated in the transitional charter.
The leaders relocating to Mogadishu are frustrated by the fact that President Yusuf has announced that he will use soldiers loyal to him to create a secure environment in Jowhar, while Mogadishu will continue to struggle with its own security problem.
Some government members, mostly Somali warlords, even threatened to launch an attack on Jowhar if President Yusuf establishes his offices here.
President Yusuf, however, has not been impressed by these threats, telling the press he "came to Jowhar and will operate from here."
Yusuf has appealed for militia across the anarchic nation to join a security force for his government.
Addressing supporters in Jowhar earlier in the week, President Yusuf confirmed he was finally setting up a temporary base for his government there until security improved in Mogadishu.
"I appeal to militia in Mogadishu and its environs to join government forces to be part of the national security," he said.
"My government is recruiting armed forces for Somalia in 15 regions," the Somali leader said.
"The government will continue its reconciliation drive; its main objective is to return law and order," he added.
With threats from some warlords in Mogadishu, including government members, to attack Jowhar if Yusuf takes troops there, analysts fear the rift at the heart of the new Somali administration could turn violent and jeopardize the gains which have been made so far.
The transitional government was formed after two years of a peace process in Nairobi that brought together factional leaders, elders, civil society representatives, and others to work out how to end almost 15 years of war.