Katanga was made a general in the Congolese army early in 2005 by Joseph Kabila, the president, as part of a power sharing deal with militia leaders that ended Congo's devastating 1998-2002 civil war.
But he was arrested two months later in connection with the killing of nine UN peacekeepers in northeastern Congo in February 2005.
He is believed to have been in custody ever since, though he has never been tried for the slayings.
Katanga's ICC warrant was unsealed on Thursday, after Congolese authorities who had been detaining him turned him over and sent him to the Netherlands, where he was transferred to the ICC's detention unit built inside a Dutch prison near the country's North Sea coast.
The only other suspect in the cell block is Thomas Lubanga, head of a rival militia from the same region of Congo, whose trial on charges of recruiting and using child soldiers in Ituri is expected to start early next year.
Lubanga's will be the first trial at the ICC, which was set up in 2002.
ICC prosecutor Luis Moreno-Ocampo said the court was investigating more brutal crimes in Congo.
"Today a second person from [Congo] is in custody, and he will not be the last one to face justice in the ICC," he said. "Perpetrators must know they will be prosecuted."
But the fact that Katanga was already in Congolese custody before his arrest - as was Lubanga before him - highlights one of the ICC's recurring problems: its inability to get its hands on suspects not being held by co-operative governments.
Warrants for senior government or militia leaders in Sudan and Uganda have not been enforced.
"The issue of arresting people remains a challenge for the ICC," the court's deputy prosecutor Fatou Bensouda said.
The court has no police force to execute arrest warrants and instead has to rely on co-operation from other states in detaining suspects.