"They are not speaking to anyone ... there was no fighting, the pro-government forces left last night."
Abdiqadir Osman, a spokesman for Somalia's president, confirmed that there had been no fighting in Mahaday.
"Our troops were not defeated. No fighting took place," he said.
"We have withdrawn from the city because of military tactics and will return to it when we want to."
The Somali government has been losing ground in recent weeks and now controls little more than the centre of the capital, Mogadishu, with the support of African Union troops.
Hizbul Islam has pledged to fight AU troops in Somalia until they leave the country and topple Sharif Ahmed, the president.
Al-Shabab, the other rebel group which seized control of Jowhar, is listed by the US state department as a "terrorist organisation" with links to al-Qaeda, a designation that the group denies.
Mohamed Abdullahi Omaar, Somalia's foreign minister, told Al Jazeera that the armed opposition groups were still far from taking over control of the country.
"The capital city is firmly in the hands of the government ... substantial areas of the regions are also in our hands," he said from Washington DC.
Omaar said that although Jowhar and Mahaday had been captured, government forces had been able to fight off attacks on other routes into Mogadishu.
"This is a military front and therefore ebbs and flows take place in different forms," he said.
"They may have come into the towns, but these people are not necessarily coming on the basis of taking over territory. They come in, disrupt and go out."
The clashes between government forces and rebel fighters have forced many Somalis to flee west across the border into Kenya.
"Refugees have risked everything to escape the fighting in Somalia. Now some are telling us they would rather take their chances in Mogadishu than die slowly here"
Joke Van Peteghem, head of MSF mission in Kenya
A charity said on Monday more than 270,000 refugees in Kenya were facing alarming shortages of food, water and shelter in overcrowded camps.
Medecins Sans Frontieres (MSF) said up to 5,000 people were arriving every month at three camps in Kenya's Dadaab area.
"The situation is simply scandalous," Joke Van Peteghem, the MSF head of mission in Kenya, said.
"These refugees have risked everything to escape the fighting in Somalia. Now some are telling us they would rather take their chances in Mogadishu than die slowly here."
Somalia has not had an effective government since 1991, when Mohamed Siad Barre was overthrown by armed groups who then turned on each other.