"We, ourselves, are behind the problems and we are accountable in this world and in the hereafter. Islamists have been capturing all towns and now control Elasha. It is every man for himself if the government collapses," Yusuf said.
"The Islamists kill city cleaners, they will not spare legislators."
Yusuf blamed his government's ineffectiveness partly on disagreements between him and Nur Hassan Hussein, Somalia's prime minister.
Somalia has failed name the new cabinet despite being urged to do so by leaders from the Inter-Governmental Authority on Development (IGAD) - Ethiopia, Djibouti, Kenya, Somalia, Sudan and Uganda - at a meeting in October.
"The prime minister gave me a list of new cabinet ministers but I do not know how to approve names of those who destroyed our government when the constructive ones were excluded," Yusuf said.
Hussein said Yusuf bore the responsibility for the crisis within the government.
"The Somali president is responsible for the failure of the transitional federal government to achieve its goal of forming a new cabinet," he told reporters in Nairobi.
"It is unfortunate that the president has become the first to oppose the IGAD [Inter-Governmental Authority on Development] directives though he was one of the signatories."
The president's remarks came after witnesses said that fighters from the al-Shabaab movement had captured the port town on Barawe, about 180km from the capital Mogadishu.
Earlier in the week the group seized the nearby town of Merka, which has a strategically important airstrip.
Even in Mogadishu, which remains nominally under government control, al- Shabaab fighters carry out public punishments, conduct training exercises and present themselves as an alternative government.