As a result, over 3,000 private and 200 regular students, who had passed their intermediate exams in third division, would not be able to continue their studies.
Earlier, when educational institutions in Islamabad were affiliated with University of Punjab, they provided admission to almost every student who had passed the intermediate exam, and also registered them with the university irrespective of their division.
A faculty member of a college, who is also member of the admission committee, said it was not possible to refuse students who are eligible for admission under a quota just because they had low marks.
"Usually, students having good marks do not apply in federal government (FG) colleges. Most of the students who get admission either have a C or a D grade. There are also admissions under sports, teachers, Fata/Fana and special children quota," he said.
"Students, who come from Fata/Fana, usually pass in third division but we provide them admission because they come under a quota," he added.
He said there were PhD professors in the federal capital that had completed their intermediate or graduation in third division.
Had they been refused to continue studies, we would never have had these PhDs, he added.
A student of H-9 College, requesting anonymity, said the management had told him that since the college was affiliated with QAU this year, he could not be registered with the university because he had passed his intermediate in third division.
"If we cannot be registered with QAU for the exams, why were we admitted in the college? It seems door to education is being closed on us," he added.
Mohammad Bilal, a student who could not apply for the admission because of his job, said: "I was thinking of sending private admission for the graduation exam, but now it seems the QAU will not allow me to sit the exams because I had passed intermediate in third division," he said.
Controller Examination, QAU, Dr Shahid Ansari confirmed that last month the university had sent a letter to colleges in which the minimum criterion for registration was set at 45 per cent.
"We are running a world-class university and have to ensure merit. University seats can remain vacant, but we cannot give admission in violation of merit.
Some medical colleges, including the Quaid-i-Azam Postgraduate Medical College, are affiliated with us and they follow the merit of 45 per cent," he said.
FG College Teachers Association Spokesman Tahir Mahmood said normally affiliated departments make their own merit. In FG colleges, there is 45 per cent merit at the master's level, but at graduation level, students with third division were also acceptable.
Riaz Khan, father of a student, said: "My son has been admitted in third year because seats were available in the quota meant for students from Fata. Now the management says the QAU has refused to accept his registration.
"Children from Fata cannot get good marks because of war and unavailability of facilities. They should not be prevented from pursuing further education."
A teacher of F-10/4 College said: "New admissions for BA, BSc and BCom were completed in August. It is now difficult for institutions to cancel these admissions because it will become an issue. Students may approach the courts and a new issue will emerge."
"Ministry of Capital Administration should have finalised these issues before announcing affiliation of educational institutions with QAU. Students have been paying Rs2,000 sports fee in addition to the usual registration and admission fee but they are being discouraged from getting education," he said.
Director-General, Federal Directorate of Education, Dr Shahnaz A. Riaz said she was unaware of the situation and would look into it on Monday.
"It is a big issue because education of students should not suffer. I will conduct an inquiry as to why such issues had not been cleared before announcing the affiliation," she said.
Vice-Chancellor, QAU, Dr Masoom Yasinzai said he would see if such a letter had been sent to the colleges after admissions.
"I will definitely find a way out for the students because their education should not suffer," he said.