The girl's mother, who is chairwoman of Sweden's Muslim Council, was informed by the foreign ministry on Tuesday night that her daughter had been put on a plane back to Sweden, Svenska Dagbladet reports.
Benaouda is one of at least four people from Sweden to be arrested in Kenya after fleeing the recent war in Somalia.
Following their arrest, the group was first flown back to Somalia before being moved on to a prison thought to be located in Ethiopia.
"We are working to gain access to them," Carl-Magnus Hyltenius from the foreign ministry told Svenska Dagbladet.
Two British human rights organizations, Reprieve and Cageprisoners, came into the possession of a passenger list from a secret transportation of prisoners that was carried out on January 27th.
A Kenyan passenger plane left Nairobi for the Somali capital, Mogadishu. The plane travelled the same route twice, transporting a total of 63 prisoners, all of whom were handcuffed and blindfolded. Four of the passengers were Swedish citizens.
The prisoners were accused of fighting on the side of the Islamist militia against Somali government forces and their Ethiopian allies.
Two months have passed since Helena Benaouda first heard that her daughter had been arrested.
Safia Benaouda travelled to Dubai with her fiancé during the Christmas holidays. There they met another group of Swedes, and together they made the journey to Dubai to Somalia.
The reason for their departure from the Arab emirate to the troubled African nation has not yet been established.
As yet there has been no explanation for the release of Safia Benaouda. Her fiancé remains in captivity, as do the two other Swedish citizens arrested in the same operation, .
"I have not heard anything about my husband," the 33-year-old wife of one of the prisoners told Svenska Dagbladet.