The 22-year-old student had reportedly been held hostage at gunpoint for more than three weeks in a secluded basement near Bodh Gaya, Buddhism's holiest site in east India.
Calcutta police commissioner Pallav Kanti Ghosh told BBC that two men who said they were brothers, Sajid Khan, 32, and Jawed, 25, approached the tourist and told her they were tour guides. One of them allegedly spoke in "very fluent Japanese."
The men are suspected to be part of an organized gang known for targeting female tourists traveling alone. The brothers were arrested on Friday "for confining and raping the Japanese student," the deputy superintendent Alok Kumar Singh said. Three others were arrested shortly after for their involvement with the case.
The alleged victim was able to escape after her health suffered enough that was taken to a hospital.
"When her health condition deteriorated due to repeated rape and poor living conditions, she was brought to Gaya [town] for medical treatment on 20 December," a police officer told AFP.
The woman was able to escape, and contacted other Japanese tourists who helped her reach out to the Japanese consulate in Kolkata. She then traveled to the city from Gaya.
The Bodh Gaya complex houses one of the oldest Buddhist temples still standing in India and attracts tourists from across the world. The student is thought to have been living and studying in rural india for many months.
India has come under scrutiny after numerous high-profile incidents of violence against women in recent years, including the fatal gang-rape of a woman on a bus in New Delhi in 2013.