"The girl breathed her last at the Capital Hospital last night," local police station in-charge officer Asim Panda said.
Chief Minister Naveen Patnaik announced Rs 10 lakh ex-gratia for the family of the victim.
The girl, from Kharinasi village under Mahakalpara block in Kendrapara district, struggled for survival for 12 days at the SCB Medical College Hospital in Cuttack after being set ablaze on July 28, police sources said.
Doctors took her by ambulance to the Bhubaneswar airport last night to fly her to the Safdarjung Hospital in Delhi, but the attempt failed after the victim's condition deteriorated, sources said
The girl, a 7th standard student, was then rushed to the Capital Hospital in Bhubaneswar, where she died.
The police arrested 21-year-old Eakadashi Das and 20-year-old Pradip Das for setting the girl ablaze and for attempted rape, sub-divisional police officer, Human Rights cell, Kendrapara, Shantanu Kumar Padhee said.
They were arrested under Section 307 (attempt to murder) and 376 (rape) of IPC.
"Following the death of the girl, we slapped Section 302 of IPC (murder) against them," he said.
The SDPO said that the dying declaration of the girl was recorded in the presence of a magistrate.
Another person was also involved, he said.
Soon after her death, protesters damaged and torched vehicles in different parts of Bhubaneswar early this morning, police sources said.
Ambulances were also damaged at the Capital Hospital, besides two buses and a truck, they said.
Director General of Police Prakash Mishra ordered the deployment of 20 platoons of forces in different areas of the state capital.
The protesters also demonstrated before Chief Minister Naveen Patnaik's residence and the official residence of Health Minister Damodar Rout.
In Kendrapara district, roads were blocked for an hour at Kendrapara, Ramnagar, Mahakalpada and Rajnagar, said Sub Divisional Police Officer Nrusingha Charan Swain.
The Bharatiya Janata Party had called a 12-hour state-wide bandh on Sunday to protest the government's 'apathy' toward the girl.
"The BJD government has failed miserably in providing safety and security to women. The chief minister should resign as he has lost all right to remain in office any longer," senior BJP leader Surama Padhy said.
"The chief minister must resign on moral grounds as his government is responsible for the death of the girl. She died due to government apathy," Odisha Pradesh Congress Committee President Jayadev Jena told reporters.
Jena, who had visited the Capital Hospital on Friday night, said Health Minister Damodar Rout should also resign for failing to save the life of the girl.
He said the state government should have sent the girl to Safdarjung Hospital in Delhi immediately.
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