The development comes as 40 aid agencies, including Save the Children, World Vision, Oxfam and the International Medical Corps, warned of an impending humanitarian crisis in the country, according to news agencies.
Seven people including a child were killed in the Jowhar attack, resident Abdi Ali Osman told Reuters.
A spokesman for the Islamic Courts forces, Abdirahin Isse Addow, told the news service from an undisclosed location that four government soldiers were killed in the fighting.
"Our troops entered Jowhar at six in the morning. Few government troops fought us and we defeated them, forcing them to run away," he said.
The fighters had taken over four smaller towns and a military checkpoint near the capital Mogadishu, but Jowhar is the most significant to date. The town, located about 55 miles north of Mogadishu, served as a temporary base for the country's interim government in 2005.
Meanwhile, the group of aid agencies warned of a "catastrophic" humanitarian crisis in Somalia, which is deteriorating dramatically, the BBC reported.
"For too long, the needs of ordinary Somalis have been forgotten," the agencies said in a joint statement, urging the "international community and all parties to the conflict to urgently focus their attention on the catastrophic humanitarian crisis in Somalia."
The agencies said 2 million Somalis need daily help to survive the crisis and that the fighting between Islamist and government forces in Mogadishu is forcing 20,000 people from their homes every month, according to the Associated Press.
Somalia has been without an effective government since warlords ousted President Mohamed Siad Barre in 1991 and then turned on each other.
In June 2006, an Islamist militia called the Somalia Islamic Courts Council took over Mogadishu.
Ethiopia intervened to help Somalia's government, and the Ethiopian and Somali force drove the Islamists to the country's southernmost tip in December 2006.
The U.N. Security Council plans to discuss the situation in Somalia on Thursday, according to the BBC.
Last week, U.N. Secretary-General Ban Ki-moon presented the council with a report that outlined several proposed scenarios for the U.N. to step up its presence in Somalia, including deploying 27,000 peacekeepers.
The current African Union peacekeeping force in Somalia, known as AMISOM, is made up of about 2,400 members from Uganda and Burundi -- out of a planned 8,000-strong force, according to the Agence France-Presse.
To enhance the prospects for peace in Somalia, "there should be a viable political process that would run concurrently with a peacekeeping process," said Sarjoh Bah of New York University's Center on International Cooperation, which recently published its annual review of global peace operations for 2007.
Stabilizing Somalia politically would mean engaging all stakeholders, including former Islamic Courts members, while not compromising on international standards for human rights, said Bah.
In addition, the international community must give financial and logistical support to the AU forces currently in the country, he said.
AMISOM operates with the United Nations' approval and its mandate is set to expire in August.