"So far witness have only said that Khalif was wounded in the attack and then hospitalised," he said.
Khalif is among 11 people who recently had their assets frozen by the US governmentfor alleged involvement in "terrorism" and is on a UN list of people subject to sanctions because of their involvement in the violence in Somalia.
According to the UN Security Council, Khalif, has raised funds for al-Shabab and was involved in two car bomb attacks in the capital in April 2008.
An al-Shabab official had no precise death toll figure but said that "scores of people were killed and wounded".
Witnesses told the Associated Press news agency that most of the victims were worshippers.
"The blood stained the walls and human flesh was scattered everywhere," Isma'il Dahir, a businessman, was quoted as saying.
Sheikh Ali Mohamud Rage, an al-Shabab spokesman, blamed "mercenaries hired by the so-called government of Somalia" for the blasts.
"We are investigating the situation. This kind of action will not be left unanswered. On behalf of the Muslim people of Somalia and on behalf of Allah we will retaliate against this crime," he said.
There was no immediate claim of responsibility.
The attack was the second bombing at a mosque in the market in less than a week.
Al-Shabab and a number of allied groups control much of southern and central Somalia as well as large parts of the capital.
The government views the Bakara market as stronghold of al-Shaba and the Hizbul Islam movement. Over the last three years the market has seen near-daily shelling as the fighters have clashed with African Union and Somali soldiers.
The transitional government controls only small areas of Mogadishu, but has repeatedly said that it is preparing to launch an offensive against anti-government groups in the capital.
Somalia has not had an effective government since 1991, when Mohamed Siad Barre was overthrown by armed groups who then turned on each other.