The Maldives government said its hands are tied in the case, and there is no way to stop the punishment from being carried out, CNN reported Wednesday.
Registrar Zaima Nasheed Aboobakur said the girl, whose name was not reported, will remain in a children's home for the time being.
"We have explained to her how if she wants to receive the punishment (the lashings) right now she can ... or it can be postponed until she turns 18," Aboobakur said.
Abbas Faiz, a researcher with Amnesty International, said the ruling against the girl is an outrage because she is allegedly a victim of sexual abuse at the hands of her stepfather.
"She has been sexually abused and at the same time she has been charged with an offense. ... We are really outraged at this punishment," Faiz said.
"Confession from a child who has really gone through some damaging experiences cannot be taken as evidence," he added. "If she had said no, then the only case that would have gone forward would have been the charge of sexually abusing a minor against the stepfather."
Masood Imad, a spokesman for the president, said the government considered the teenager a victim and she should not be flogged but it could not intervene in her sentencing.
"We cannot just send a memo to the judiciary and say, 'Don't lash anybody hereafter.' It doesn't happen that way any more. We have to talk with them, get them to understand, get them to initiate the laws or we initiate the laws together and then pass it to the Legislature," Imad said.