Their comments represent a fresh challenge to government plans to use foreign troops to stabilise the war-torn country.
African soldiers due to arrive in the coming months were unacceptable on the grounds of faith, said Ibrahim Suley, Secretary-General of the Umbrella Organisation of Islamic Clerics, a federation of Mogadishu Muslim groups.
"We reject all foreign intervention and request parliament not to approve the peace mission, which will allow African forces to enter Somalia," Suley said in a statement.
"We are not of the same religion and that is why we cannot accept them."
The statement echoes complaints by two Mogadishu tribal leaders serving in President Abd Allah Yusuf's cabinet about his plan to rely on African Union (AU) troops to restore order.
The federation has support among some of the poorest communities in the capital and links to influential Islamist courts in the Sunni Muslim country.
Yusuf's government asked for
the deployment of 7500 troops
The tribal leaders say Somali militias, given retraining, can do the job themselves and in any case foreigners who do not share Somalis' faith or culture will find it difficult to keep order.
Yusuf's government, formed in the safety of neighbouring Kenya at peace talks last year, aims to end fighting between clans and militias that have run Somalia since feuding tribal leaders ousted Muhammad Siad Barri in 1991.
Law and order
It plans to return to Somalia from Nairobi on 21 February and will probably rely on its own resources for security in its first few weeks. But it wants a foreign peace force to arrive to help it restore law and order within a couple of months.
Somalia's insecurity was underlined this week when BBC producer Kate Peyton was shot dead in one of the capital's less risky neighbourhoods. At least eight other foreign journalists have been killed in Somalia in the past 14 years of chaos.
Armed men working for Yusuf's government combed several districts of Mogadishu on Thursday and Friday and picked up several leads in the search for the killer, residents said.
Yusuf is seen by some as being
too close to Ethiopia
Yusuf's cabinet has asked for 7500 troops from African Union and Arab League nations, and the AU has authorised five east African nations to send troops and equipment.
Minivans toured the capital on Friday morning asking ordinary people to meet after noon prayers at a stadium to show their opposition to the planned deployment of AU peacekeepers.
Suley's statement made no mention of troops from the Arab League, which Yusuf has also asked to send troops.
Diplomats say the opposition to foreign troops voiced by two tribal leaders in Yusuf's cabinet - Housing Minister Usman Ali Ato and Commerce Minister Muse Sudi Yalahow - reflects mistrust of Yusuf's intentions rather than confidence in their own militias.
Yusuf is seen by many in Mogadishu as being too close to regional power Ethiopia, Somalia's historic foe.
Dozens of MPs who visited Mogadishu this week in a team led by parliament speaker Sharif Hasan Shaikh Adan were due to arrive back in Nairobi on Friday and report to the government.
"We have to put down our guns voluntarily," Adan told a radio talk show in Mogadishu on Thursday evening.
He added: "If that does not happen, the new system we have established in Nairobi should take appropriate measures. Our system should function with the support of the international community, including African countries and their armed forces."