The decision to hike the fee was taken recently and will be effective from January next year.
The protests, which began yesterday, ended this morning after a meeting between the students and management in which an assurance was given that their demands will be looked into.
Shouting slogans against the IIT management, a group of about 300-400 PhD students gathered at the administrative building yesterday and didn't let Director Partha Pratim Chakrabarti, Registrar Pradip Pyne, Dean of students and a number of other senior officials leave their office the whole night till their demands were met.
"They have been increasing rates regularly but this time the hike was very steep," she added.
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Another student claimed that IIT Kharagpur's rates are the highest among all the IITs despite the town being a cheaper place to live in.
"I get Rs 25,000 monthly stipend and have a family to run. How will I manage my expenses?," he asked.
Defending the move, registrar Pyne said, "The IIT has around 11,500 students enrolled in various courses out of which about 2,500 are research scholars. Only 300 of those scholars were protesting. We have assured them that we will address their concerns."
The hike in the hostel rates are applicable to all the students but there were hardly any protest by undergraduate or post-graduate student, he claimed.
"Most of our research scholars do not come from an IIT background. Protests like this is not a part of our ethos. We are always open to discussions with students," another institute official said.
In April this year, a large number of students at IIT Kharagpur had stated a peaceful protest against the HRD Ministry's decision to hike fees.