Kushayb is the first Sudanese suspect taken into ICC custody in The Hague. The court issued an arrest warrant for him in 2007, accusing him of persecution, murder and rape in the western Sudanese region of Darfur between 2003 and 2004.
ICC chief prosecutor Fatou Bensouda hailed Kushayb's transfer - almost 20 years after his alleged crimes - as a long overdue milestone.
"The victims in the Darfur situation deserve to finally have their day in court," she said in a statement.
Prosecutors say Kushayb was a top commander of pro-government Janjaweed militias that led attacks on towns and villages and is implicated in at least 199 murders and the forcing of 40,000 mainly Fur civilians from their homes.
There was no immediate public comment by Kushayb on the accusations against him.
The conflict in Darfur killed an estimated 200,000 people and drove 2.5 million from their homes. The United States said killings there amounted to a genocide. The ICC has not accused Kushayb of that crime.
A government source in Central African Republic said Kushayb had been arrested in the northern town of Birao and sent by plane to The Hague on Tuesday morning.
Former Sudanese President Omar al-Bashir is also wanted by the ICC. He faces charges of genocide, war crimes and crimes against humanity for atrocities committed by pro-government forces in Darfur.
The ICC has no police force and relies on its 123 member states to carry out arrest warrants.
The UN Security Council referred the situation in Darfur to the ICC, the world's first permanent war crimes court, in 2002. Five other arrest warrants related to Darfur are still outstanding including that of Bashir.
The ICC did not say when Kushayb would first appear before the court.