According to a report in The New York Times, a military spokeswoman said the military would not provide lawyers for the men because the charges did not have any relation to their work as soldiers.
The Guardian reports the men could receive prison sentences of between 16 and 30 years.
The girl, a member of the Embera community, was found Monday after going missing from her home.
Human rights activist Aida Quilcue said, We know that this is not an isolated issue.
Colombias military has a long history of abuse against women and Indigenous people.
Colombia must be merciless with sexual abusers of minors, adolescents and women, Marta Lucia Ramirez, the countrys first female vice president, posted on Twitter.