The bench, headed by Justice Dipak Misra and comprising Justices A M Khanwilkar and M M Shantanagoudar, also directed the institutes to give an undertaking that such error will not be repeated.
"IITs will have to give an undertaking and develop a mechanism that such mistakes will not recur and ensure that no such situation arises in which bonus marks will have to be awarded to all the students," the bench said.
It said that on careful study of the Gurunanak Dev University case verdict, it was revealed that there was no negative marking, while in the present case there was negative marking for wrong questions attempted by the students.
The apex court had on July 7 restrained the IITs and other institutions from conducting further counselling and admissions saying the court will go by its earlier judgement of 2005 and bonus marks cannot be given to those who have not attempted the wrong questions.
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During the hearing, Attorney General K K Venugopal assured that IITs will devise a mechanism that such sitution will not arise in future for which bonus marks have to be awarded to students across the boards for wrong questions.
The apex court also restrained the High Courts from entertaining any petitions regarding counselling and admission through IIT-JEE (advance)-2017 to avoid any confusion.
IITs clarified that 33,307 students have taken admission and deposited their fees and classes are going to start from July 19 and only 31 seats of general category are left.
Senior advocate Kapil Sibal, appearing for some of the candidates who took the examination, said that those students who had correctly attempted the question were set to lose while those who wrongly attempted the question would gain.
Explaining the matter through a chart, Sibal said those who did not attempt the wrong question at all were also set to gain by the award of marks across the board while those who attempted correctly will be losing the highly competitive race where every single mark matters.
He said there was no malafide on the part of IITs and hence 18 bonus marks in total was awarded to students across the board for the wrong questions.
To this, the bench observed that such mistakes should not occur in future and no situation should arise for which bonus marks have to be awarded to the students.
Counsel for IITs said the JEE has the same difficulty level for all the students and it is not easy for some or tougher for others.
He said the 2005 verdict cannot be applied in this case and the apex court should vacate its stay and allow the counselling and admissions to continue.
Sibal said if the rank list was not quashed, it would affect around 4000 students who will be out of the highly competitive examination.
IITs contended that an experts' body of 33 persons from various institutes, who met twice, had decided that award of bonus marks to the students across the board was the only solution to the problem.
Therefore, across the board bonus marks were given to the candidates, Venugopal had told the court, adding that otherwise the IITs would have to strike down the marks.
The AG had earlier said it was difficult to re-evaluate the answersheets of over a lakh students who took the exam and awarding of bonus marks across board was the most practical solution.
The apex court had on June 30 issued notice to the Ministry of Human Resource Development on a plea seeking quashing of the IIT-JEE 2017 rank list.
Since then several other students had approached the apex court seeking quashing of rank list.
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