Several new ministers from outside parliament have been appointed, including the ministers of defence and finance.
Abdullahi Yusuf, the president, approved the appointments.
Mohamed Mohamoud Guled, the interior minister, lost his position while Ahmed Abdi Salan, co-founder of the Horn Afrik media corporation and a Somali-Canadian, was appointed deputy prime minister and information minister.
The list of ministers was not immediately available and Hussein did not say when the last three members would be named.
In December, Hussein dissolved a bigger cabinet after five ministers quit.
It dashed Hussein's plans to move forward after his own appointment, which followed the resignation of Ali Mohamed Gedi after a political battle with Yusuf.
Yusuf's aides blamed the stress of the rift with Gedi for a chest complaint, with some saying he was near death after he was flown last month to neighbouring Kenya for treatment.
He denies reports of serious illness.
Yusuf, 73, is a long-surviving liver transplant patient and has gone abroad several times for specialised treatment.
He has now travelled to Addis Ababa, the Ethiopian capital, for treatment.
"The president was flown to Addis Ababa for medical reasons," a government official said.
"He was well-dressed and he got on the plane by himself. He was not very ill."
Yusuf reportedly left on Thursday, and would be flown to Nairobi, the Kenyan capital, "if his condition gets serious".
Yusuf's administration faces a long-running conflict in Mogadishu that has lasted since government forces, backed by the Ethiopian army, defeated fighters loyal to the Union of Islamic Courts from Mogadishu last year.
The fighters have since been waging attacks in the capital, displacing hundreds of thousands of people.