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 General Augusto Pinochet's dictatorship.
Mr Pinera's government has opposed any easing of the ban.
"I've asked the health minister to personally look after the (girl's) health," Mr 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 this week 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."