Somalia says it has not agreed with Kenya for its troops to enter the south of the Horn of Africa nation to fight Islamist rebels, but would form a security committee to work with Nairobi.

Somali President Sheikh Sharif Ahmed objected to the 11-day Kenyan incursion in comments on Monday and Kenya in turn demanded an official clarification of the Somali government's position on Wednesday.

Ahmed's comments sparked condemnation from some Somalis, especially in southern areas where Kenyan troops have taken control of towns from al Shabaab, and worried Western nations that back and fund the Somali government.

"Kenya gives us logistic support and trains our troops, but we have not agreed for their troops to cross our border," Ahmed told a news conference. "Our Somali troops have the ability to fight al Shabaab in Somalia."

Kenya sent troops into Somalia 11 days ago to fight the Islamist rebels, blamed by Nairobi for a series of kidnappings on Kenyan soil and frequent border incursions that threaten the east African country's security.

The Kenyan troops, advancing on several fronts towards al Shabaab strongholds, are working with Somali government soldiers and allied militias in the region. They have taken several towns but have not yet had a major showdown with al Shabaab fighters, who are regrouping and bolstering defences at strategic points.

In a clarification statement, the Somali government said it had only agreed with Kenya to cooperate in undertaking a coordinated military operation spearheaded by Somali soldiers trained by the Kenyan government.

The statement issued by the Ministry of Information stopped short of calling for Kenyan troops to leave Somalia, however.

"We all share the need to defeat and destroy al Shabaab. No one wants to see the demise of al Shabaab more than the people of Somalia," it said.

"We also share the attitude that al Shabaab constitutes a common enemy to both countries and in this regard, the sovereignty and the territorial integrity of both Somalia and Kenyan should be respected," the statement said.

The Somali government said Prime Minister Abdiweli Mohamed Ali had been assigned to appoint and head a joint security committee to work with the Kenyan government.

"Kenya will help us and there will be understanding," Ali told the same news conference. "We have agreed with Kenya to coordinate with us in the operation against al Shabaab, logistics and information sharing."

Earlier on Wednesday, Kenyan Internal Security Minister George Saitoti called for a clarification of the Somali position "as it is essential to have a unified approach in dealing with the destabilisation of Somalia by al Shabaab".

The Somali statement said the government was committed to ridding the whole country of al Shabaab and establishing local administrations in any liberated areas.