Bolivia's outgoing President Eduardo Rodriguez has sacked the army chief and ordered a probe into the destruction in the US of some 30 missiles in October.
Gen Antezana had said he was responsible for the decision
Mr Rodriguez said he had been told the ageing Chinese missiles posed a safety risk and had authorised American help with their decommissioning.
But, he said, the army should not have sent them out of the country.
At the time, Evo Morales - who will take office on Sunday - had called it a US plot to weaken Bolivian defences.
Mr Morales' party had threatened to impeach President Rodriguez over the deactivation of the surface-to-air missiles, but correspondents says it has backed away from the threat recently.
President Rodriguez said on Tuesday he would seek clarification from Washington about the episode.
Defence Minister Gonzalo Mendez has resigned so his role can be investigated.
Army chief General Marcelo Antezana will face disciplinary proceedings after he published a letter in several newspapers, demanding that the government release the documents pertaining to the decommissioning.
In October, he had issued a declaration saying he was the sole person responsible for the decision.
But last week, he appeared to reject any responsibility and hinted that there had been American pressure for the missiles to be taken to a US base.