The head of Somalia's National Olympic Committee confirmed to the BBC that she had died but did not say how.
Samia competed in the 200m event at the Beijing Olympics in 2008 despite having almost no formal training.
Although she came in last place, several seconds behind the other competitors, BBC's Alan Johnston in Rome says it is extraordinary that she was able to take part at all.
She had grown up and trained in the Somali capital, Mogadishu, facing war, poverty, a complete lack of athletics facilities and prejudice from some quarters against women participating in sports.
According to a profile of Samia on al-Jazeera, she faced death threats and intimidation when she returned to Somalia after the 2008 Olympics, with the Islamist militia al-Shabab controlling parts of the capital.
In October 2010, the runner is reported to have moved to Ethiopia in search of a coach to help her train for the London 2012 Olympics. What happened between then and her apparent death in the Mediterranean Sea is unclear.
According to al-Jazeera, there were no guarantees that she would be accepted to train at the stadium in Addis Ababa - it was dependent on her running times and permission from the Ethiopian Athletics Federation.
Reports in Italian media suggest she may have been hoping to find a coach in Europe who could help her reach the London Olympics.
Italian newspaper Corriere Della Serra says Samia's fate only came to light when former Somali Olympic athlete Abdi Bile brought it up at a talk.
He mentioned Mo Farah, the Somalian runner who moved to the United Kingdom aged 12 and triumphed in this year's Olympics.
Quote
"We are happy for Mo - he is our pride", he said. "But we will not forget Samia".
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