A Somali warlord, who has returned to the peace process in neighbouring Kenya, says he will not contest presidential elections next month.
Mediators feel it would be better if General Morgan was involved in the peace process
General Morgan's forces battled those of a rival faction around the southern port of Kismayo earlier this month.
He was the only major faction leader not taking part in the parliament tasked with electing a president.
Some rival warlords are questioning whether he should be allowed to join the parliament now.
The parliament is due to elect Somalia's first president in 13 years by 10 October, but Gen Morgan was not nominated to be an MP because of his absence.
He says he is prepared to wait to see how the power-sharing posts in the transitional administration are allocated.
"I'm not one of the people seeking to be elected as president," he told the BBC's Focus on Africa programme.
Mediators, however, feel that the peace process would be stronger if Gen Morgan were inside, rather than outside.
"All those who can make a contribution should be here to make a contribution and that is the only way for Somalia to move ahead," the African Union's representative at the Somalia talks, Mohammed Ali Faum, told the BBC's Network Africa programme.
Gen Morgan denied reports that he had been injured in the fighting around Kismayo.
"That was cheap propaganda... I just decided not to fight," he told Reuters news agency.
Somalia has not had a functioning national government since 1991, since when the country has been divided into fiefdoms, controlled by rival warlords, who occasionally battle for territory.
Mr Faum said that he was confident that these peace talks would succeed where many others have failed in recent years.
"What has happened so far has given great cause for hope," he said.