The country's 26 universities and 52 technical and vocational education colleges have so far registered only 90,000 out of the 212,000 students who qualified for free higher education.
Kagisho Mamabolo, spokesman for the National Student Financial Aid Scheme, said this week that it had not received confirmation from the institutions whether a further 122,000 students who qualified for financial aid had been admitted or registered.
"NSFAS will depend on institutional confirmation before processing any sort of payment to these students' institutions."
He said institutions supplied them with information on registrations in a format required by NSFAS as soon as the registration period closed.
"Not all institutions have submitted [the information]; the submission is ongoing. It cannot be done overnight. The universities must make sure that the registration is done correctly.
"We will settle the bill of the student as and when the university brings it to us because processing any sort of payment without confirmation means we might be paying a university for a student who was not admitted."
Finance Minister Malusi Gigaba announced during his tabling of the national budget this week that higher education institutions will receive R57-billion over the next three financial years to fund free tertiary education for the poor and working-class students.
Gigaba was forced to scramble for money to fund free higher education following former president Jacob Zuma's sudden announcement of the programme in December last year.
A random survey by the Sunday Times this week found that 16 of the 26 universities enrolled 98081 first-year students this year...