In the refutal, the Presidency reiterated that a commission of inquiry into higher education funding headed by Judge John Heher was appointed and the president waited for the commission to conclude its business.
The Commission was established to explore the feasibility of fee higher education.
"The President has tasked the Inter-Ministerial Committee on Higher Education Funding headed by Minister Jeff Radebe and the Presidential Fiscal Committee to process the Heher Commission report and advise him on how to respond to the content thereof".
Among the Commission's recommendations are that government looks into online learning as a solution.
Instead, the Commission recommends state-guaranteed loans for university students, to be paid back only when a graduate reaches an acceptable salary level.
The State will repay each student loan to the bank at a given date (say five years from the first advance).
The report also recommends that the government increase its expenditure on higher education and training to at least one percent of the GDP, in line with comparable economies.
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To implement this model, the commission recommended that the existing National Student Financial Aid Scheme (NSFAS) model be replaced by the new income contingency loan system. The Commission further recommended that government pay particular attention to the Technical and Vocational Education and Training colleges as they can not perform at their current funding levels. Those cuts might include social grants for the most vulnerable and the budgets for housing, infrastructure and the armed forces, the newspaper said.
The Presidency has denied this.
The long-awaited fees report has finally been released.
Zuma should now clarify what role the report will play in his plans for the sector going forward, DA MP Belinda Bozzoli said in a statement on Monday.
At the time, Zuma said he was studying and working on the report's contents and consulting the relevant ministers, excluding Nzimande, who was sacked by Zuma in his cabinet reshuffle in October.
Zuma is expected to release his findings after studying the Heher report soon.
The reports had said that the president had been looking for funds amounting to around $2,7bn (£2bn) from the treasury to fund higher education.