Officials with the Supreme Islamic Council of Somalia (SICS) said the conference of scholars and peace activists from al-Islah group in a Mogadishu hotel was illegal as it had not been approved.
Speaking after heavily armed men broke up the meeting on Thursday, a SICS spokesman said the meeting was not licensed and the organisers did not have permission to hold it.
Abdul Karim Ali Muddey said: "We have to be a community ruled by laws. People must seek permission to have a meeting, and we will licence it as long as the forum is not a threat to public safety or Islamic teachings."
Members of al-Islah, a charity that operates Muslim clinics and schools throughout Somalia, confirmed that the meeting had been disbanded but declined to discuss the matter further.
The agenda for the conference was not clear, but the group has been pushing for a resumption of dialogue between the Islamists and Somalia's increasingly weak and marginalised transitional government.
Arab League-mediated talks between the two sides due to resume this week in Khartoum failed to take off after the Islamists demanded a delay and the withdrawal of Ethiopian soldiers alleged to be in Somalia to back the government.
During the first round of talks in June, both sides agreed to cease fire and recognise each other, but they have since traded accusations of violations.
Since 1991, Somalia has been
without a central authority
The rise of the Islamists, who seized Mogadishu from regional commanders in June after months of fierce fighting and have rapidly expanded their territory since, poses a serious threat to the government's already limited authority.
As they have moved beyond the capital, the Islamists have begun to enforce a strict interpretation of Shariah (Islamic law), closing down cinemas and photo shops and punishing what they consider to be un-Islamic behaviour.
Somalia has been without a functioning central authority for the past 16 years since the 1991 ousting of Mohamed Siad Barre.