Morales previously acknowledged he had a child with his ex-girlfriend Gabriela Zapata during a two year affair but claims she told him the infant died shortly after birth.
Zapata is now at the center of a corruption scandal shaking his administration, and in a plot worthy of a telenovela, her aunt revealed last week that the child was not dead, but alive and well.
"We are absolutely convinced that sadly, the boy has passed away," Defense Minister Reymi Ferreira said Tuesday. He said Morales asked for Zapata's family to prove any claim to the contrary.
"An appeal has been filed with the child magistrate, calling for the child to be produced by the family, privately, within five days," Ferreira added.
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He also said damages were being sought "to put to rest any doubt anyone may have, and for it to be seen who is lying."
She faces charges of money laundering, embezzlement and abuse of influence, prosecutor Edwin Blanco said Sunday.
Zapata, who until recently was a senior manager at CAMC, entered into a relationship with Morales in 2005 when she was 18 years old. Morales said it ended two years later.
A reporter's bombshell disclosure last month of the previously unpublicised relationship set off an investigation into influence peddling just weeks before Bolivia was to vote on whether to change the constitution to allow Morales to run for a fourth term.
A congressional committee is investigating the contracts awarded to CAMC, and opposition members of congress have called for Morales and Zapata to testify.
The opposition accuses Morales of favoring Zapata, and insists their relationship lasted at least until 2015, despite Morales' denials.
The president has said their child would now be eight or nine years old, and that he would like to raise the boy if he were alive. Morales has a son and daughter whom he has recognized, from previous relationships.