Somalis are already struggling with drought and war
There is no confirmation from Washington, but the encounter comes amid growing speculation that, after Afghanistan, Somalia could be the next target for US attacks.
On Monday, Somalia's interim Prime Minister, Hassan Abshir Farah, strongly rejected American charges of al-Qaeda bases in his country.
The militia leaders, from the Rahanwein Resistance Army, told the BBC they had discussions with 13 officials, including nine US officers, on Sunday night in the town of Baidoa, about 250 km north-west of the capital, Mogadishu.
They said they told the officers about a training camp near the border with Kenya run by a Somali Islamist group, al-Itihad.
Washington says it has evidence of definite links between the al -Qaeda network and al-Itihad.
A local faction leader said it was now up to the Americans to decide what to do.
Escape routes
On Monday, US Deputy Defence Secretary Paul Wolfowitz said the administration was trying to "observe, survey possible escape routes, possible sanctuaries" for al-Qaeda members who may attempt to flee Afghanistan.
Mr Wolfowitz said Somalia was an obvious choice. "It's a country virtually without a government, a country that has a certain al-Qaeda presence already," said Mr Wolfowitz.
Denying the US allegations, Somali Prime Minister Hassan Abshir Farah told the BBC there would be no justification for air strikes against his country.
"We have sent to the Bush administration a letter of invitation to come here to see what is here... We are ready to fight against the terrorists," he said.
But the BBC's Ishbel Matheson says the US is not prepared to accept the denials.
US troops are said to be deploying to Kuwait as part of preparations for a Somali campaign.
Already a US warship has been stationed off the Somali coast and there have been reports that surveillance flights have been carried out over the country.
Mogadishu's transitional government controls only parts of the capital and Washington fears that the absence of state authority makes Somalia a potential haven for extremist groups.