Shaikh Hassan Dahir Aweys said the presence of Ethiopian troops sent to reinforce Somalia's government had ruined any chance for peace.
Aweys said: "Until Ethiopian troops leave Somali soil, we will never negotiate with the government."
Earlier on Tuesday, the government had agreed to attend unconditional peace talks in Khartoum.
This followed a meeting between the government and Francois Lonseny Fall, the UN special representative to Somalia, in Baidoa, 240km northwest of Mogadishu.
Shortly before Aweys' announcement, Abdirizak Adam, President Abdullahi Yusuf's chief of staff, said: "We will go to Khartoum without any preconditions."
Fall later arrived in the capital, Mogadishu, which is controlled by the Islamic group.
He attended prayers with two Islamic officials, Shaikh Ahmed Shaikh Sharif and Shaikh Yusuf Indohaadde.
Talks between the two sides to prevent a standoff from escalating into war broke down on July 22, when the Islamists pulled out because of a reported incursion into Somalia by Ethiopian troops to defend the fragile interim government.
Fall's visit came a day after the African Union (AU) urged the UN Security Council to speed up plans to ease an arms embargo on Somalia to allow foreign peacekeepers to deploy.
The appeal followed an agreement by the AU and the east African regional body IGAD to send troops to help to secure peace in Somalia.
The plan has been repeatedly rejected by the Islamists, who control Mogadishu and a large swath of southern Somalia after defeating US-backed secular regional chiefs early last month.