General Ernesto Cedeno, the prosecutor, told state television that the military was investigating whether public funds went missing during Baduel's tenure as defence minister.
"This is no sort of political retaliation ... simply an investigation under the law," Cedeno said, urging Baduel on Thursday to co-operate in the probe to "clarify the situation" within the judicial system.
He did not specify whether charges had been filed.
Baduel said on Wednesday that military officials had come to his home to say they had opened a judicial process against him.
He said he had been "charged" but was unclear for what crime.
He said the investigation was "eminently political" and accused prosecutors of following orders that trickled down from Chavez and the current defence minister.
"This has no judicial significance," Baduel said. "Just the political purpose of trying to shut me up, to frighten me."
Baduel played a key role last fall in leading opposition against a constitutional reform package that would have allowed Chavez to run for re-election indefinitely.
Venezuelan voters rejected the reforms in December.