The teen gave birth to a baby girl after the incident, which took place eight years ago, Cesar Siles said.
"We have observed with indignation serious crimes that seek to go unpunished. I am referring specifically to a girl, a girl raped at the age of 15, 16," the minister told a press conference.
"The father recognized on the birth certificate" of the child is the 64-year-old Morales, he said, adding: "This is under investigation."
Morales, who served from 2006 to 2019, is mired in a scandal that erupted this week when a prosecutor said she was fired for seeking his arrest as part of a probe into human trafficking that involved a minor.
The paperwork seeking his arrest, which was leaked to the press, said that in 2016, then president Morales had an affair with a 15-year-old girl with whom he had a daughter.
Without referring to this case, Morales wrote on X: "I am neither surprised nor worried. All the neo-liberal governments, including the current one, threatened me, persecuted me, jailed me, tried to kill me. I am not afraid! They will not silence me!"
A judge shelved the request to arrest Morales and the prosecutor who presented it, Sandra Gutierrez, said she was later sacked.
Morales, a former coca grower who became Bolivia's first Indigenous president in 2006, was extremely popular until he tried to bypass the constitution to seek a fourth term.
He went on to claim victory in a 2019 election marked by allegations of fraud but was forced to resign after losing the support of the military, and then fled the country.
Bolivia's current president, Luis Arce, used to be close to Morales and served as his finance minister for more than a decade. But they fell out and are now fighting each other for leadership of the ruling MAS party to be its candidate in elections next year.
Courts have said Morales is not eligible to run.
