President Sheikh Sharif Sheikh Ahmed has vowed to introduce Sharia law
One of Somalia's hardline Islamist leaders and the information minister have both told Osama Bin Laden not to interfere in Somalia's affairs.
The al-Qaeda leader on Thursday called for Somalia's president to be toppled.
Sheik Hassan Dahir Aweys, who denies US charges he has links to al-Qaeda, has been reported as saying only Somalis should decide on their future.
Information Minister Farahan Ali Mohamoud said Bin Laden should concentrate on his own survival.
"We know that bin Laden has his own problems in the mountainous area of Tora Bora where he is hiding, so he has no place making such statements at a time when Somalia is keen to emerge from 21 years violence," the AFP news agency quotes the information minister as saying.
Bin Laden's call was published by known militant websites on Thursday, although there has been no independent confirmation of its authenticity.
President Sheikh Sharif Sheikh Ahmed, a moderate Islamist, was inaugurated in January after UN-brokered reconciliation talks.
He has promised to introduce Sharia law to the strongly Muslim country.
But hardliners in the al-Shabab movement say his version of Sharia will not be strict enough and have continued to fight against his government.
They, and other Islamist groups, now control much of southern and central Somalia.
The 12-minute audio recording of Bin Laden - entitled "Fight on, champions of Somalia" - carried an often-seen image of the al-Qaeda leader with a map of Somalia in the background.
It accused Mr Ahmed of having "changed and turned back on his heels... to partner up with the infidel" in a national unity government.
"This Sheikh Sharif... must be fought and toppled," the tape said, before comparing the Somali leader to "the [Arab] presidents who are in the pay of our enemies".
This is Osama Bin Laden's third tape this year
It was Bin Laden's third broadcast this year.
Mr Ahmed was a leader of the Union of Islamic Courts which controlled Mogadishu in 2006 before being ousted by Ethiopian forces, backing the previous Somali president.
Mr Aweys was also in the UIC but the two have since split.
"Somalia knows [its] future and who can involve, but it is not something for Osama Bin Laden and al-Qaeda either," he reportedly told Arabic TV.
Somalia, a nation of about eight million people, has not had a functioning national government since warlords overthrew President Siad Barre in 1991 and then turned on each other.
As part of a UN-brokered deal to reconcile moderate Islamists and dissident lawmakers in a unity government, Ethiopian troops withdrew in January.
President Ahmed has the support of several Islamist groups but al-Shabab has continued to fight the Somali government and the African Union peacekeepers in Mogadishu.