"The process is very, very important," he told a special session of the conference. "The process by itself could actually jeopardise what we have achieved up to now, if it is the wrong process. I would like all of us to think much more creatively and very intensively about how best to avoid the mistakes that have been made in the past."
He stressed the transitional nature of the future government. "It is not THE government of Somalia, because that has to be done by all the people of Somalia."
He also said the work of six technical committees should be completed by next Monday. The Inter-Governmental Authority on Development (IGAD), which is mediating the talks, would then take five to seven days to harmonise the reports and try to iron out contradictions.
The technical committees have been working since December on core issues of the Somali conflict, including federalism, disarmament, land rights and conflict resolution.
Kiplagat announced the appointment of Kenyan Major General Joseph Musomba to oversee an international monitoring committee for a ceasefire agreement signed by the Somali sides last October.
Musomba told IRIN he hoped his diplomatic and military experience would allow him to "do a good job", and that UN support would be needed to help enforce the ceasefire.
FACTION LEADERS ABSENT
After the special session, Kiplagat went into a closed-door meeting of the leaders' committee, which was expected to discuss "future structures and a road map" for implementing the structures.
However, a number of key faction leaders have been absent from the conference for some time, including prominent Mogadishu-based faction leaders Muse Sudi Yalahow, Muhammad Qanyare Afrah and Usman Hasan Ali Ato. Also missing are representatives of the Kismayo-based Juba Valley Alliance, which controls much of the Juba valley area of southern Somalia, and faction leader Muhammad Habeb, who controls Jowhar in the Middle Shabelle region.
The leader of the self-declared autonomous region of Puntland, Col Abdullahi Yusuf, left for Somalia on Monday. None of these leaders has indicated whether he will return or not.
"Their absence is likely to take away some of the significance of today's meeting," a regional analyst close to the talks told IRIN on Tuesday. "The significance of the meeting will be proportional to the representation at the table. Without full representation, the value of the process is diminished."
He said IGAD should insist on full representation of the leaders or call for a recess. He stressed that the Sudan peace talks, also underway in Nairobi, could provide a good guide to follow.
"There have been a number of recesses in the Sudan talks, and it has done wonders for the progress of the talks," he noted.
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