Other militant groups the students are affiliated with includes the Taliban group and Hezb-e-Islami party led by Gulbuddin Hekmatyar.
The distressing report was emerged during a visit by presidential advisor Qamaruddin Shenwari who was leading a delegation to Nangahrar province.
He told BBC that their findings shows the university students are linked with the enemy circles which also includes a number of the university lecturers.
This comes a large group of the students organized a rally in Jalalabad, the capital city of Nangarhar few days earlier and carried flags belonging to Taliban, ISIS and Hezb-e-Islami party.
This comes as the Afghan Intelligence operatives detained at least 27 university students who were affiliated with the anti-government armed militant groups.
NDS said last week that the university students were arrested after they torched the national flag and instead raised the flags of ISIS and Taliban group.
According to NDS, a number of the detained university students also have links with Hezb-e-Islami Party led by Gulbuddin Hekmatyar.
The group was looking to organize further illegal demonstrations in a bid to disrupt the situation in Nangarhar and particularly in Nangrhar University, NDS said, adding that the suspects were arrested during a joint operation conducted by Afghan police and intelligence operatives.