Mr Ble Goude was first put under UN sanctions in 2006, accused of inciting attacks against UN personnel.
Mr Ble Goude's lawyer, Kwame Akufo, told the BBC that Ghana had not followed the proper procedures for extradition.
They said Mr Ble Goude was handed over to authorities in Ivory Coast, where he was taken into custody.
Mr Ble Goude denies leading pro-Gbagbo militias who attacked foreigners and northerners during the unrest which followed disputed elections in 2010.
Several Gbagbo allies have gone into exile in Ghana and they first reported that Mr Ble Goude had been arrested on Thursday.
Ivory Coast's former youth minister and ally of former President Laurent Gbagbo, Charles Ble Goude, has been extradited from Ghana, officials say.
Last week Mr Ble Goude was extradited to Ivory Coast from Ghana.
Later, the Ivorian government said in a statement that Mr Ble Goude was apprehended "in a joint police operation between Ghana and Ivory Coast".
Ivory Coast's former youth minister and ally of ex-President Laurent Gbagbo, Charles Ble Goude, has been charged with war crimes, murder and theft of public funds.
Last year, Mr Ble Goude told the BBC that, as head of the Young Patriots group, he had only organised rallies and meetings and never run a militia.
Last year, Mr Ble Goude told the BBC that, as head of the Young Patriots group, he had only organised rallies and meetings and had never run a militia.
Dywedodd Brian Thornton o Gymdeithas Rheoli Colegau eu bod nhw eisoes wedi bod yn gwneud arbedion effeithlonrwydd ers nifer o flynyddoedd ac nad oedd yn glir ble y buasai'n bosib gwneud arbedion pellach.
The Ivorian Popular Front (FPI), Mr Gbagbo's party, condemned the charges in a statement and called for Mr Ble Goude's "immediate release" in order to improve the prospects of talks being held between the FPI and the government.
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