"I am shocked and deeply anguished at the latest incident of sexual assault and rape of a five-year-old child in Delhi. I join her family in praying for a speedy recovery and call upon concerned authorities to ensure the best possible medical attention for her," Rashtrapati Bhavan spokesperson Venu Rajamony quoted the President as saying.
"As a society, we must introspect at the erosion of values and our repeated failure to ensure the security of our women and children," he said.
The president, who approved anti-rape bill earlier this month, said "we must identify the causes and find solutions for such criminal depravity in our midst."
"Let us pledge to put all our energy and effort into ensuring that such aberrations which stain our moral fibre and standing as a society is prevented".
The five-year-old girl was abducted on April 15 and kept hostage for two days without food and water in a room on the ground floor of the building in east Delhi's Gandhi Nagar.
The accused Manoj Kumar, 25, was arrested from a village in Bihar's Muzaffarpur district today.
Meanwhile, the brutal sexual assault has brought protestors out on the streets again.
A large number of protestors gathered outside Delhi Police Headquarters today, demanding the commissioner's resignation.
Holding up banners and shouting slogans against the government and police, protestors demanded that Delhi Police Commissioner Neeraj Kumar resign, saying he "failed to tackle the rape crimes" in the city.
The protestors also shouted that the rapist should be given the death sentence.
A man protesting outside the police headquarters said: "The government makes laws just for the sake of making them, with no intension to stop crimes. None of the laws are implemented, and we see rapes increasing by the day."
"After the Dec 16 gang-rape, the police appears to have learnt nothing at all. We hear of two or three incidents each day. How long will this continue? The accused must be punished, and police must be pushed to be more vigilant," a young protestor said.
Protestors also thronged the All India Institute of Medical Sciences (AIIMS) where the five-year-old victim is under treatment.
Doctors said that she had been responding to treatment, and her condition had stabilised. The girl will require corrective surgery of her private parts. Detailed examination of the five year old was done by a team of eight doctors.