West Bengal chief minister Mamata Banerjee said the case was being transferred from local police to the Central Bureau of Investigation (CBI) given the "sensitivity" of Friday's attack on the nun, who was raped during a robbery at a convent.
"Police are making their best efforts," Banerjee, the state's top official, said on Twitter.
"(But) Considering the seriousness and sensitivity of the case, I have decided to entrust investigation of the case to CBI."
She also pointed to West Bengal's close proximity to Bangladesh as a reason for the shift, amid local media speculation that the robbers may have fled across the border.
The referral came just hours after the head of the Catholic church in India demanded swift justice for the nun, who is in her 70s and who needed surgery after the rape.
While local police have taken several people in for questioning, no one has been formally arrested over the incident, which has again highlighted the frightening level of sexual violence in India.
After visiting the victim in hospital as well as the convent where she was attacked, Cardinal Baselios Cleemis voiced frustration at the lack of progress in the investigation.
"I would like to request the authorities to ensure justice is done," said Cleemis, president of the Catholic Bishops' Conference of India.
"The sisters have forgiven but justice (should) be made visible and such acts should not happen again," he told reporters in the town of Ranaghat.
"I understand that the process has begun... but I'd like to request the chief minister (Banerjee) to adopt a faster approach and ensure justice is meted out at the earliest."
The nun was attacked around midnight when a gang of robbers broke into the convent near Ranaghat and ransacked the premises.
Although police have launched a gang-rape inquiry, officers say only one person sexually assaulted the nun, who is expected to be shortly released from hospital.
Detectives have released CCTV footage showing the faces of several members of the gang, fuelling frustration that charges have not been forthcoming.
Protests were held in West Bengal and also in the capital New Delhi on Tuesday, while Banerjee was confronted by hundreds of protesters late Monday when she visited the victim.
Deputy police superintendent Ajoy Prasad told AFP on Wednesday the nun had recorded her statement, and also confirmed that a hunt for multiple offenders was still under way.
The incident adds to a grim record of sexual assaults in India, which this month banned a documentary about a December 2012 gang-rape that sparked domestic and international outrage.
It is also the latest in a string of attacks on churches or Catholic schools, and came despite a pledge by the Hindu nationalist Prime Minister Narendra Modi to ensure the safety of religious minorities.
Modi has said he was deeply concerned about the attack on the nun.
A CBI spokesperson said the national government, including the home ministry, must approve West Bengal's request that it take up the case before it could act.
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