The two sides had been due to meet in Sudan today for a second round of talks aimed at resolving differences that threaten to plunge the nation further into conflict, but the government said it would not attend.
Even as an Islamist delegation left Mogadishu for Khartoum to show
commitment to the talks, President Abdullahi Yusuf Ahmed said they could not be trusted.
"The (Islamic) courts (union) violated the previous agreement signed in Khartoum," he told lawmakers in Baidoa, where the transitional government is based due to insecurity in Mogadishu.
"The most important parts were the recognition of each other and cessation of hostilities," Mr Yusuf said.
He accused the Islamist militia of violating both these provisions and of plotting to "attack Baidoa and the southern port of Kismayo".
The Islamists' supreme leader rejected the charges and accused the government of sheltering members of a US-backed warlord alliance.
Sheikh Hassan Dahir Aweys, a hardline cleric branded an "extremist" by the country's transitional government and a "terrorist" by the United States, said the Islamists had merely finalized their seizure of Mogadishu begun in early June.
Despite the accusations, a 15-strong delegation from the Islamist union, the Supreme Islamic Council of Somalia (SICS), headed for the talks in Khartoum.
"We are interested in getting peace," chief SICS negotiator Ibrahim Hassan Adow said before leaving with his team and a group of officials from the Arab League, which is sponsoring the talks in Sudan.
The Khartoum meeting is part of international efforts to restore peace and stability to Somalia which has been without a functioning central authority since 1991.