The problem of strays is now dogging the IIT-Kanpur where several dog bite cases have taken place in recent days.
A section of faculty members and other officials have demanded a ban on stray dogs on the premises.
The institute's animal welfare cell had already decided to remove the dogs and dog feeders alleged that they were being harassed.
"Dogs have been mysteriously disappearing from the campus," they said.
Refuting the allegations, IIT-Kanpur director Prof Abhay Karandikar said: "We are not against stray dogs. We have an animal protection cell within the campus. The authorities have discussed the matter at length, and decided to let stray dogs stroll in the open areas such as gardens, but not near hostels."
He said that eight to 10 students had submitted a representation to Animal Welfare Board of India (AWBI) stating that they would like to continue feeding the dogs.
"An AWBI team was to visit the campus for an inspection on Wednesday. But it did not turn up. We have 13 hostels where 9,000 students reside. Their safety is important. Dogs have also attacked peacocks on the campus," he said.
Prof Karandikar added the institute was not against dogs, and only wanted to restrict their movement near hostels.