Abdi Hassan Awale, was arrested after Somalis in the Nordic country recognised him and reported him to police, said Gillian Nilsson, an organiser of the conference.
Awale, also known as Abdi Qeybdiid, was the commander of clan leader Farah Aidid's troops that fought American peacekeepers in Mogadishu in the early 1990s.
One of those confrontations in 1993 was featured in the book and film Black Hawk Down, and left 18 US soldiers and hundreds of Somalis dead.
Suspicion of genocide
Police spokesman Karl Sandberg would not confirm the suspect's identity, but said he was arrested early on Monday at a hotel in Lund and was brought to the west coast city of Goteborg to be questioned by prosecutors.
Sandberg said the 57-year-old man was arrested on suspicion of genocide, although police did not specify what crimes he had allegedly committed.
Police in Goteborg questioned him on Monday, his lawyer, Pieter Kjessler said.
"We have to clarify this legal situation. It may be more complicated than investigating the actual charges"
"He claims that the accusations are false," Kjessler told Swedish public radio.
Kjessler said the interrogation was interrupted because the suspect did not trust the translator who was provided and demanded to meet members of the delegation that he travelled to Sweden with.
Awale, who was a colonel in Somalia's former army, was named interior minister in the former unrecognised government that was declared in the capital after Mohamed Siad Barre's removal in 1991.
The interior minister in Somalia's divided government appointed him as the national police chief, but the prime minister named another person to the same position.
Nilsson said Awale was part of a six-member Somali delegation headed by Parliamentary Speaker Sharif Hassan Shaikh Aden that attended the conference on development in the Horn of Africa.
Police spokesman Mats Glansberg said prosecutors have until Thursday to decide whether to ask a court to keep the man detained. He said it was unclear whether a foreign citizen suspected of genocide can stand trial in a Swedish court, or whether he would be extradited to an international tribunal.
"It is very complicated," Glansberg said. "We have to clarify this legal situation. It may be more complicated than investigating the actual charges."