Passengers and officials at the airport in southeastern Libya said the men identified themselves as members of a Darfur rebel group - the Sudan Liberation Movement, which promptly denied any involvement.
But Murtada Hassan, executive director of Sun Air, which owns the jetliner, said their motives were personal and they had no connection with any political or rebel groups. He would not elaborate.
The hijackers, Darfuri men in their 40s, made no political demands.
"Their first demand was France. ... Then they negotiated for Libyan asylum. Then they had no other solution - there was no escape," said Mohammed Al-Balla Othman, Sudan's consul in the desert oasis of Kufra, where the plane landed Tuesday.
It was unclear whether their asylum request would be granted.
The plane was hijacked about 20 minutes into its flight from Nyala, the capital of southern Darfur, to Sudan's national capital, Khartoum.
Waving handguns, the men forced their way into the pilot's cabin. Passengers said the men threatened to blow up the plane, but there was no indication they had explosives or any other means to cause an explosion.
The plane landed at Kufra, a World War II-era outpost near Libya's border with Egypt and Sudan, where about 500 security personnel and police surrounded the plane as negotiators worked to free the passengers.
Late Wednesday, a Libyan plane flew the freed crew and passengers to Khartoum. The hijackers remained in custody for questioning.
Among the passengers were former rebels who have become members of the Darfur Transitional Authority, an interim government body responsible for implementing a peace agreement reached in 2006 between Sudan's government and one of the Darfur rebel factions.
One of them, Muhammad al-Tijani al-Tayyib, said the hijackers pushed officials out of the first-class cabin and announced they were taking over the plane.
"I heard all the goings-on. It was rational and calm," he said. "Still, we spent a terrible night, obviously, in fear."
Only two hijackers surrendered, but possible accomplices might have slipped out with the freed passengers, said Hassan, the Sun Air director.
The hijacking took place not far from a Darfur refugee camp that the Sudanese military attacked on Monday, raising questions about whether the men were rebels who acted in retaliation.
The government stopped short of blaming Darfur rebels for the attack, but officials said the incident would likely exacerbate tensions in the region.
Speaking to reporters in the southern city of Juba, Sudanese President Omar al-Bashir called the hijacking "a cheap terrorist act." Sudan's Foreign Ministry called for the hijackers to be extradited.
Darfur's ethnic African rebels have been battling the Arab-led Khartoum government in a five-year conflict that recently prompted the International Criminal Court's prosecutor to press genocide charges against al-Bashir. He is accused of crimes against humanity, for allegedly unleashing government-backed militiamen on civilians and refugees.
The attack Monday by the Sudanese military on the refugee camp was the deadliest clash in months.
A spokesman for Darfur's U.N.-African Union peacekeepers, Nourredine Mezni, said at least 33 people killed in the attack were buried Tuesday, though some U.N. officials said the toll could be higher.
A spokesman for one of the rebel groups, the Justice and Equality Movement, Ahmed Hussain, said he had reports of 70 dead. He accused the government of being behind the hijacking, saying it was trying to "divert attention" from Monday's attack.
