The boy reportedly took the girl to a nearby government school, where, the family says, he raped her in the toilet.
The police has arrested the accused, who has been identified as 20-year-old Tahir Ahmad of Mir, a vehicle mechanic.
Sumbal: Four days after a youth was arrested for allegedly raping a three-year-old girl in Bandipora district of north Kashmir, police sources said preliminary medical examination has revealed he is not a minor.
Authorities appealed for calm after the protests, which followed a pledge by Muslim clerics in the region to dedicate their Ramadan sermons to women's rights.
Malik directed the IGP to work swiftly in the case and ensure that the culprit gets exemplary punishment.
According to the Baramulla police, at least 47 security personnel were injured during a violent clash between protesters and security forces, on the National Highway in North Kashmir's Baramulla district on Monday.
On Monday, allegations emerged that the principal of another school issued a certificate for the accused that he was a minor, sparking anger and triggering protests across the Kashmir valley. A youth in Mirgund area was seriously injured in clashes with security forces.
Schools and shops across the Kashmir Valley shut spontaneously thousands of people joined the demonstrations to demand that the alleged culprit be executed.
The protesters threw stones at the security forces, who fired tear gas at the demonstrators.
Students of Kashmir University, Central University and the Islamic University of Science and Technology boycotted classes and held protests. "Fresh reports of pellet gun firing on protestors, yet another reflection of continued Indian atrocities", he said. "We will request a team of senior doctors to determine the age of the accused through scientific medical investigation".
"Mortified to hear about the rape of a three-year-old in Sumbal".
People's Conference general secretary Imran Reza Ansari described the incident as a crime against humanity and demanded severe punishment to the accused. Declaring the certificate fake, police said the accused is not a juvenile. "All of Kashmir stands in unison", said Mr. Farooq.