The move has been delayed for nine months amid concerns over security in the Somali capital, Mogadishu.
Some have called for UN peacekeepers to be deployed in Somalia to stop armed militias disrupting the transition.
President Abdullahi Yusuf arrived in Jowhar in central Somalia where he was welcomed by hundreds of locals.
Kenya’s president hosted a farewell party, though a deep rift remains over where the government will be based.
