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(Adds Information Minister paragraphs 12-13)
By Sahal Abdulle
MOGADISHU, March 22 (Reuters) - The Somali government said on Thursday that al Qaeda had made a young militant Islamist commander its leader in Mogadishu as fighting raged for a second day in the coastal capital.
Deputy Defence Minister Salad Ali Jelle told a news conference Aden Hashi Ayro -- an Afghanistan-trained commander in his 30s who runs the Islamists' feared Shabab, or military wing -- was personally directing the growing insurgency.
"The government is being targeted by those who used to work with terrorists, the so-called Islamic Courts," Jelle said. "And after they had a long consultation with al Qaeda, they named Aden Hashi Ayro as head of (al Qaeda) operations in Mogadishu."
The United States and the Somali government have long accused Ayro, and other Islamist leaders, of links to al Qaeda. But some critics say the government paints its political rivals as terrorists to secure more backing from Washington.
Thursday's accusation came as insurgents again battled Somali government forces and their Ethiopian military allies, forcing hundreds of families to flee in the worst fighting in the Horn of Africa nation since a war at the end of 2006.
After heavy clashes on Wednesday that killed at least 16 and saw soldiers' bodies dragged through the streets and burnt, fighting reignited in the city when Ethiopian tanks guarding a Somali government base opened fire on unidentified attackers.
Witnesses said the cannons thundered repeatedly over a 10-minute period, followed by the clatter of machineguns around the base, situated in a former defence department headquarters.
ECHOES OF U.S. MISSION
A separate gun battle also raged in the northern Ramadhan neighbourhood, witnesses said. And a huge explosion was heard in the government-controlled Kilometer Four area mid-afternoon.
It was not clear if there were any fresh casualties from Thursday's clashes. But hundreds of residents -- mainly women and children -- fled the fighting with their belongings on donkey carts, minibuses and trucks.
The defence department base has been a favourite target of gunmen who launch almost daily hit-and-run attacks on the government and its allies, including about 1,200 African Union (AU) peacekeepers from Uganda who arrived this month.
It and the Ramadhan neighbourhood were strongholds of the Islamist movement that ruled Mogadishu and its environs for the last half of 2006, until the government and Ethiopian soldiers defeated them and took the capital just before the New Year.
Information Minister Madobe Nunow Mohamed said government forces had arrested a number of insurgents and captured "a lot of arms" in a disarmament drive that started on Wednesday.
"The Transitional Federal Government had been patient for a long time, while remnants of the Islamic Courts Union were shelling government positions, economic institutions and civilian neighbourhoods on a daily basis," he said.
Wednesday was one of the bloodiest days in Mogadishu since the government took the city from the Islamists.
The grisly scenes recalled the aftermath of the 1993 downing of two U.S. Black Hawk helicopters by Somali militiamen during a failed American operation to capture a warlord.
The images of dead American troops being dragged through the streets helped prompt the pullout of U.S., and later, U.N. peacekeepers who were battered by militia attacks.
Though many believe the insurgents are defeated Islamists, analysts say criminals, warlord fighters and clan militiamen have also joined a loose coalition opposing the government.
The former leader of the Islamists, Sheikh Hassan Dahir Aweys, surfaced in public for the first time since the war calling on Somalis to remove their foreign "occupiers."
In a telephone interview, Aweys told the BBC's Somali language radio section that he was still inside the country.
"Somalia is under occupation and people have the right to remove occupiers," he said. "The Islamic Courts should have been commended for returning law and order, but the international community failed to do so."
(Additional reporting by Farah Roble; and Yasin Bu'ul in Baidoa)