The two sides last met in Khartoum on June 22 where they agreed to stop military campaigns and recognise each other.
But the talks stalled amid government allegations the Islamists had broken the pact against military expansion, and Islamist claims of foreign interference in Somalia.
On Saturday, diplomats and delegates gathered at a hall in Khartoum for the talks which officials said could take days.
Mohamed Mohamud Guled Gaamadheere, Somalia's new minister of public works and housing, told Reuters: "We expect [talks] to last around 10 days or so, depending on what happens."
The Arab League is leading the talks, hoping to convince both sides to share power after the Supreme Islamic Courts Council took over the capital, Mogadishu, and a swathe of southern Somalia.
Its rise has challenged the authority of the fragile Western-backed administration, which is based in the provincial town of Baidoa.
Sharif Hassan Sheikh Adan, the parliament speaker, is heading the government's delegation while the Islamist team is headed by Ibrahim Hussein Adow, who is in charge of foreign relations.
Somalia was plunged into anarchy after the 1991 ousting of Mohamed Siad Barre by commanders who then proceeded to fight over patches of the country.