"You know in Somalia today everyone thinks he or she is right and doesn't want to dialogue. We must abandon this culture. We must sit together, talk and come up with solutions to our problems," Ahmed said.
"That is the best way forward. We must stay away from anything that will bring further conflict."
Ahmed's Alliance for the Re-Liberation of Somalia (ARS) joined the transitional government as part of a peace deal signed in 2008.
But the administration has little real power, with armed opposition groups, including al-Shabab, controlling many towns and large areas of the capital Mogadishu.
As the parliament met in neighbouring Djibouti to elect Ahmed, al-Shabab, which split from the Islamic Courts' Union over the peace process and disapproves of Ahmed, moved into the of Baidoa were the government normally meets.
"It is true that al-Shabab and the radical elements believe that Sheikh Sharif is a traitor, he is engaged with the arch-enemy of Somalia, Ethiopia, and the West," Rashid Abdi of the International Crisis Group think-tank told Al Jazeera.
"They paint him as a man who has, basically, sold out.
"It will be very, very difficult for Sheikh Sharif to engage in dialogue with the radical Islamist groups in southern Somalia, but essentially these are his former comrades in arms, so we should not stop him from making that attempt," he said from Nairobi, the capital of Kenya.
Ahmed insisted that his experience as leader of the Islamic Courts' Union during their brief period of power had prepared him for the task of stabilising the country, which has been without an effective central government since 1991.
"When I begun that task many used to tell me that I would fail and that I should abandon my lofty ideas for peace. These calls came to me from friends, relatives and all those who knew me," he said.
"But I was adamant that I could not just sit and watch as Somalia's situation continued to worsen. Thanks God I managed to convince many to accept peace and we realised stability for sometime under the Islamic Courts' Union.
"I believe there is even a bigger opportunity for peace today."
There have been more than a dozen previous peace efforts since Mohammed Siad Barre was overthrown in 1991 and three previous governments have been formed, but they never managed to take effective control of the country.
The African Union (AU) has sent peacekeepers to Somalia in an attempt to halt the violence, which has kiled at least 16,000 people in the last two years and caused more than one million to flee their homes.
But the forces, sent by Uganda and Burundi, have been unable to bring the situation under control and have instead become targets of some of the near-daily attacks.
|Al-Shabab fighters control many towns and large parts of the capital Mogadishu [AFP]
Ahmed told Al Jazeera that during a recent AU summit, he had asked the body to review how the mission in Somalia operates after reports that civilians had been killed in the crossfire between the two sides.
"We met the African Union Commission and discussed the problems the AU forces in Somalia pose to civilians when they come under attack. We said we are not happy with how they react with force," Ahmed said.
"Somalia is passing through bad times and our intention is to give the role of peace building to the people and the government to take the leadership and facilitation of these efforts.
"We want to secure the country in a very short time. This will enable the peacekeepers to return home."