The Union of Islamic Courts (UIC), an umbrella group of clerics, on Friday blamed Yusuf for attempting to spark new fighting in Somalia by deploying hundreds of fighters allegedly trained and armed by Ethiopia in his base in the provincial town of Jowhar.
"Yusuf is not the president of Somalia but simply, he is one of the warlords who have been creating havoc in the past 14 years," UIC deputy chairman Sheikh Abdi Ali said in Mogadishu.
"How can you call a president somebody who is masterminding a fresh civil strife in his country?"
The clerics themselves own a heavily-armed militia group controlling parts of Mogadishu and a neighbouring region.
Their close links with other powerful warlords in the capital means their criticism of Yusuf is a setback for him.
Fears of unrest
Ali accused the president of "an attempt to fuel hostilities" by deploying militia armed and trained in Ethiopia to Jowhar.
The militia arrived on Tuesday night in the base of Yusuf's transitional federal government that has refused to relocate to Mogadishu, sparking fears of fresh unrest in Somalia.
"Yusuf is not the president of Somalia but simply, he is one of the warlords who have been creating havoc in the past 14 years"
Sheikh Abdi Ali,
UIC deputy chairman
The deployment prompted the United Nations to pull out 13 its international staff members from the town, 90km north of Mogadishu.
Before he was elected president in Kenya in October last year, he was a warlord in charge of the northeastern region of Puntland.
But Somali presidential spokesman Yusuf Ismail Baribari quickly dismissed the move as "nonsense" and a political bluff from extremists.
"The statement by the so-called Islamic courts is ... not in the interest of the Somali people. The TFG has a popular and political legitimacy throughout the country," he said.
UIC and allied militia control parts of Mogadishu and the neighbouring Lower Shabelle region.
They are in good terms with powerful warlord in the capital, who have refused to accept Yusuf's decision to set shop in Jowhar.
In the recent weeks, the Somali government has been split between Jowhar and Mogadishu with both sides making increasingly belligerent gestures that have prompted widespread fears of a new surge in fighting.