A BBC correspondent says Mr Yusuf, 72, collapsed on Friday morning in the seat of government, Baidoa.
Prime Minister Nur Hussein Hassan said his condition was not serious, but close aides have suggested otherwise.
In his absence, the prime minister, who took office in November, has appointed 15 members of a cabinet to replace those he dismissed last month.
"I've appointed 15 ministers and the rest of the ministers will be appointed soon. The new ministers will be sworn in tomorrow," Reuters news agency quotes the prime minister as saying.
The president, who had a liver transplant 14 years ago, was last month admitted to a Kenyan hospital, suffering from bronchitis.
Ethiopia helped Somalia's transitional government end the Union of Islamic Courts' (UIC) six-month rule over large parts of southern Somalia a year ago.
Since then the government has been battling insurgents in the capital, Mogadishu.
The UN says 60% of the residents of the capital, Mogadishu, have fled their homes because of fighting in recent months.
Somalia has not had a functioning national government since 1991.
Hassan Barise of the BBC's Somali Service says it had been feared the president's collapse would delay the cabinet appointments.
He says despite the setback to his health no-one is expecting President Yusuf to step down.