At least seven armed men on Monday broke into the home of Abdulkadir Yahya, a co-director of the Centre for Research and Dialogue, and killed him at about 2:30 am (2330GMT), said one of his guards, who did not want to be identified for fear the killers could target him.
The guard said the armed men shackled and blindfolded all five security men at Yahya's house and then went to his bedroom and shot him in the head.
The assailants also stole Yahya's laptop computer and a small bag of gold jewellery, said Abdikarim Fodare, one of Yahya's cousins, who arrived at the house after the attack.
Somalia has been without a central government since clan-based warlords overthrew dictator Mohamed Siad Barre in 1991. Warlords then turned on each other, plunging the country of seven million into chaos.
A transitional government set up in exile in the Kenyan capital last year has been struggling to organise its return.
In recent days, Yahya had made initial contacts to try to mediate in an increasingly bitter dispute between President Abdullahi Yusuf and parliament speaker Shariif Hassan Sheikh Aden, who have disagreed over where in Somalia to locate the government and whether it needs peacekeepers to establish control over the country.
Through the Centre for Research and Dialogue he co-directed, Yahya also was involved in organising the disarmament of militiamen in Mogadishu as part of efforts to enable Somalia's transitional government and parliament to establish itself in the country.
The Centre for Research and Dialogue is affiliated with the Geneva-based War Torn Societies Project International, which released a statement praising his "dedication, intelligence, humility, courage and commitment to peace in Somalia" and saying his death would not deter its efforts to help the Somali people achieve peace.