However BBC East Africa correspondent Will Ross says many Somalis find it hard to believe Mr Aubriere's version of events - for example that he walked unnoticed through Mogadishu, one of the most dangerous places in the world, for five hours.
Our correspondent says that for many people, a more believable explanation is that he was handed over by his captors, possibly after money changed hands.
France's foreign ministry also denied any violence was used and that a ransom was paid.
"Despite certain allegations and rumours, this happened without violence and France did not pay a ransom," spokesman Eric Chevallier told reporters.
Al-Shabab and Hizbul-Islam control much of southern Somalia, but analysts say al-Shabab is known for being the more radical of the two groups.
Al-Shabab fighters care little for their public image and they have carried out killings on camera.
Both groups are said to have links to al-Qaeda and have been reinforced by foreign fighters.
Somalia has not had a functioning central government since 1991.
Moderate Islamist Sheikh Sharif Sheikh Ahmed was sworn in as president in January after UN-brokered peace talks.
He promised to introduce Sharia law but the hardliners accuse him of being a Western stooge.
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