Saadi Gaddafi fled to the southern neighbouring country after the death of his father in the Nato-backed revolution in 2011.
Now in prison, he faces charges of misappropriating property by force and for alleged armed intimidation when he headed the Libyan Football Federation.
“The Libyan government received today Saadi Gaddafi and he arrived in Tripoli,” the Cabinet of Ali Zeidan, the prime minister, said in a statement.
Photographs of the 40-year-old wearing a blue prison uniform were posted on the website of a government-backed militia. Libyan news websites also ran pictures showing him with his head shaven in prison.
Niger had previously refused requests by Libyans to return him, with the justice minister saying he was “certain to face the death penalty”.
Saadi, one of Gaddafi’s seven sons, was being held by judiciary police forces, the government said. It thanked Niger for its co-operation and said Saadi would be treated according to international justice standards for prisoners.
Saadi, who had a career as businessman and professional footballer, was best known for being a playboy. His brief career in top-flight Italian football was cut short after he failed a drugs test. He is not wanted by the International Criminal Court (ICC).
The ICC has indicted Gaddafi’s most prominent son, Saif al-Islam, for crimes against humanity. Once viewed as a likely successor to his father, Saif al-Islam is held by a militia in western Libya, where he is being tried on various charges.
Fighters from the western Zintan region caught Saif al-Islam in the southern desert a month after his father was captured and battered to death by a mob in 2011. The militia has defied an order from the government to deliver him to a jail in the capital.