President Sebastian Pinera's comments caused anger on social media in a case that has ignited a heated national debate over abortion in one of Latin America's most socially-conservative nations. Abortions, even for medical reasons and in the case of rape, are illegal since Gen. Augusto Pinochet's dictatorship.
Pinera's government has opposed any easing of the ban.
"I've asked the health minister to personally look after the (girl's) health," Pinera said. "She's 14 weeks pregnant, and yesterday she surprised us all with words showing depth and maturity, when she said that, despite the pain caused by the man who raped her, she wanted to have and take care of her baby."
The girl was repeatedly raped over the course of two years by her mother's partner who has been arrested and has confessed to abusing the fifth grader. Her mother shocked Chileans recently when she defended him saying his relationship was consensual. The case was brought to police by the pregnant child's maternal grandmother in the remote southern city of Puerto Montt.
"It will be like having a doll in my arms," the girl whose face was obscured during the interview, told local Canal 13. "I'm going to love the baby very much, even though it comes from that man who hurt me."
Chile remains firmly conservative in social matters four decades after the dictatorship.
The Andean country legalized divorce in 2004, becoming one of the last in the world to grant married couples that right. The Chilean Senate rejected three bills last year that would have eased the absolute ban on abortion.
Pinera said his government is concerned about protecting the girl's health.
But experts say the girl's life is at risk and that she is not prepared to take a decision about her pregnancy.
"At that age the girl doesn't have a capacity of discernment, not even at age 14 would she have the mental and emotional capacity to discern this," said Giorgio Agostini, a forensic psychologist who has worked on dozens of child sex abuse cases.
"It's very likely that she is saying that she wants to have the baby like a living doll. We've seen this in other investigations," Agostini said. "So what the president is saying doesn't get close to the psychological truth of an 11-year-old-girl. It's a subjective view that is not based on any scientific reasoning to support it."
Former President Michelle Bachelet, the frontrunner in the Nov. 17 presidential elections, favors legalizing abortion in cases of rape or risks to the health of the pregnant woman or the child. The pediatrician who spent the past several years heading the U.N. agency for women, also referred to the child's case in a recent interview.
"She's a girl who needs to be protected and therefore I think a therapeutic abortion, in this case because of rape, would be in order," Bachelet told local Radio ADN.
In Latin America, only Cuba, Uruguay and some local governments make early abortions accessible to all women. Uruguay recently passed a law authorizing elective abortions in the first three months of pregnancy in the most liberal law of its kind in Latin America. Many countries in the region outlaw abortion in all circumstances.