The three discontinued courses are pulp and paper engineering at IIT Roorkee; and mining engineering with MBA, and petroleum engineering (dual degree) at ISM Dhanbad.
The total number of seats has also gone down to 9,784 this year from 9,867 last year.
However, new courses have been introduced at the IITs in Bhubaneshwar, Hyderabad and Gandhinagar.
Experts believe that discontinuance of unpopular courses will help reduce the number of seats going vacant. Last year, around 250 JEE (Advanced) seats had remained vacant.
"Some courses in the IITs are unpopular. Even if students opt for them, they don't pursue them with any interest and usually leave midway," said an IIT professor on condition of anonymity.
Other unpopular courses include mineral engineering with MBA and ocean engineering.
"Students prefer mainstream engineering. While all courses have their own benefits and a well-designed job market, too much specialisation at an undergraduate level is not preferred by students," said a former IIT director.