The biggest demonstration was in the capital, Mogadishu
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There have been demonstrations in Somalia's capital in protest at the arrest in Sweden of a Somali colonel.
Col Abdi Qeybdid was in Sweden to attend an international conference when he was detained at the weekend for alleged involvement in war crimes.
Under Swedish law, its courts can try suspects for genocide committed abroad.
Col Qeybdid has been appointed as Somalia's police chief by one faction of the split government based in the capital, Mogadishu.
President Abdullahi Yusuf has made Jowhar, 90km north of Mogadishu, his temporary capital as he says Mogadishu is unsafe.
But the speaker of parliament, Sharif Hassan Sheikh Aden, has set up operations in the capital, along with former Mogadishu warlords who are now members of the new government.
Angry
The BBC's Hassan Barise in Mogadishu says thousands of people and heavily armed militia gathered at a parade ground to protest about the arrest on Sunday.
The angry crowd was then addressed by cabinet ministers.
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There has been serious armed confrontations, and we can say that Abdi Qeybdid was not the worst
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"The government of Sweden should release [Col Qeybdid] as soon as possible and apologise for their wrong-doing," Homeland Security Minister Mohamed Qanyareh Afrah said.
Sweden would not be able to deliver justice as they don't understand Somalis "and their differences", he said.
Our correspondent says the Mogadishu faction accuse their opponents in Jowhar of being behind the arrest.
Another speaker, Mohamed Ibrahim Habsadeh - who controls Baidoa town, said the arrest would not help reconciliation efforts.
He urged the international community to understand that many Somalis had become embroiled in the last 14 years of conflict.
"There has been serious armed confrontations, and we can say that Abdi Qeybdid was not the worst," he said.
Col Qeybdid was a commander of troops loyal to the late warlord Mohamed Farah Aideed, who fought US American peacekeepers in Mogadishu in the early 1990s.
The Jowhar-based government does not recognise Col Qeybdid as Somalia's head of police and has appointed another man, Ali Madobeh, to the role.
This indicates the seriousness of the political differences between the two sides, our correspondent says.
Somalia has been without a functioning national government for 14 years and a transitional parliament and government, sworn in last year, has failed to end the anarchy.