Abubukar did not say how long Aweys would stay in Somalia. Aweys denies any link to terrorism.
Al Jazeera's Mohammed Adow, reporting from neighbouring Kenya, said: "It was largely an unexpected return... He is a senior cleric and has a lot of support from people in Mogadishu as well as different parts of the country.
"He was leader of the supereme council of the Islamic Courts Union (ICU), where the current president was also a political leader."
Aweys' return will have nothing to do with holding talks with the government, Adow said.
"He has come back, according to sources very close to him, to try to establish administrations in the areas under the control of Hizbul Islam, which was created earlier in the year when Sheikh Ahmed [Somalia's president] was elected."
Adow said the return of Aweys would complicate rather than salvage Somalia's political situation because "he holds a lot of power and support especially within the clans in Mogadishu".
He also represents clans that are unhappy with the formation of the new government, Adow reported.
Aweys' return coincided with a one-day international donors conference in Brussels, which is trying to help bring stability to the civil war-torn country.
The donors say that more than $250m is needed over the next year to improve security in a country that has been besieged by violence since 1991.