MOGADISHU — A long-brewing power struggle between the Somali prime minister and its president ended today with the premier’s resignation, throwing the government of the war-battered Horn of Africa nation into disarray.

Prime Minister Ali Mohamed Gedi and President Abdullahi Yusuf have been at loggerheads for months. Meanwhile, the government has drifted as Islamic insurgents attack against government troops and allied Ethiopian forces in the capital, Mogadishu.

“Prime Minister Ali Mohamed Gedi has tendered his resignation,” a deputy defense minister and a close friend of the prime minister, Salad Ali Geele, said. Mr. Yusuf later accepted the resignation.

Messrs. Gedi and Yusuf clashed over the balance of powers between the presidency and the premiership. Mr. Yusuf signed several oil-exploration deals with Chinese companies, angering Mr. Gedi, who believed that usurped his constitutional role. Mr. Gedi believed the presidency was a figurehead position, while Mr. Yusuf said that he was the head of state.

Both men jockeyed for position with Ethiopia, a regional power broker and prime backer of the weak government, and they come from rival clans. That brought Somalia’s long clan struggles and suspicions into the heart of the federal government.

Mr. Gedi’s departure means the government will be able to refocus its efforts on installing security in Somalia. But if members of Mr. Gedi’s Abgal clan — among the country’s largest — refuse to support the government, it could be further weakened. Many believe another prime minister from the clan will be named following Mr. Gedi’s resignation, which had been expected.

In Mogadishu, hundreds of demonstrators marched through the streets in a second day of protests against the presence of the Ethiopian troops in the country.

Protesters, mainly women, children, and young men, were burning tires, blocking roads with stones and logs, and shouting anti-Ethiopian slogans in parts of south and north of the conflict-wracked city, witnesses said.

Sporadic gunfire was heard in the city, and several shells could be seen flying through the air. It was unclear where they landed, or who fired them. At least one person was reported dead.

The body of a woman, who sells gas on a street in the south of the capital, was torn into pieces when a shell slammed into her, resident Osman Ali said.

Dahir Dhere of Medina hospital said six civilians with gunshot wounds were brought to his facility.

Mogadishu has been plagued by violence since government troops and their Ethiopian allies chased out the Council of Islamic Courts in December. For six months, the Islamic group had controlled much of southern Somalia, and remnants have vowed to fight an Iraq-style insurgency.