Baduel, a former close ally of Chavez who led an operation to rescue the president from a bungled coup attempt in 2002, became an outspoken critic of Chavez in 2007.
He had warned voters against a constitutional reform that would have expanded his powers and allowed him to run for re-election indefinitely.
Voters rejected the terms then but in February approved a constitutional amendment eliminating term limits for all elected officials.
Military prosecutors had first arrested Baduel in October on suspicion of mismanaging government funds during his command.
But Omar Mora Tosta, Baduel's lawyer, told the Venezuelan television channel Globovision that Baduel had already been scheduled to appear before the court on Friday and dismissed Thursday's arrest as a "hasty act".
Baduel has said the charges are "political persecution" due to his fierce opposition to Chavez.
Earlier this week Manuel Rosales, another opponent of Chavez and mayor of the city of Maracaibo, went into hiding to avoid what his supporters described as persecution as he also faces charges of illicit enrichment.