The ministry says the institutions are introducing fees to cover the cost of accommodation and utilities.
The Federal Ministry of Education says the latest increment in fees by some federal government-owned universities is not connected with the Student Loans Act.
It said the institutions raised their fees to cover the cost of accommodation and utilities.
The Permanent Secretary of the ministry, Andrew Adejo, disclosed this on Tuesday while appearing before an ad hoc committee of the House of Representatives on the implementation of the student loan law.
Some universities run by the federal government recently increased their tuition fees while others indicated plans to do so.
Mr Adejo explained that because of the dissolution of the governing councils of the institutions, the ministry had been in charge of approving fees increment in the absence of the councils.
He stated that the ministry only approved the request by the University of Lagos for fees increment but stopped approving others after President Bola Tinubu said the federal government-owned institutions remained tuition-free.
"What they (universities) collect is charges to cover the cost of accommodation, ICT, power, among others. It is the Governing Councils of the Universities that have the power to approve such charges for them.
"The only university that increased charges after the signing of the Student Loans Act is the University of Lagos. They came to the ministry with a proposal to Increase their charges because all governing councils were dissolved and we gave them approval.
"Immediately that was done, there was a resolution from the House stopping increase of fees and the president also gave a directive stopping any increase in fees and that is where it is, even though several others have brought their proposals," Mr Adejo said.
To buttress the dire financial situation some schools are in, Mr Adejo cited the case of Ahmadu Bello University in Zaria, where the ministry had to bail it out of its N1 billion electricity debt.
Hike of charges by universities
Last month, the management of the University of Lagos increased its charges, bringing the fees for the 2023/2024 academic session to as much as N240,250 depending on the courses of study and levels.
Although the federal government insists on tuition-free in its universities, the management of schools have been citing "charges" to increase fees in their schools.
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Earlier in the year, other tertiary institutions in Nigeria including the University of Benin (UNIBEN), Edo State; University of Abuja (UNIABUJA) and the University of Maiduguri (UNIMAID) had increased their fees.
Mr Tinubu had in June assented to the Act, which supports establishing the Education Loan Fund to provide interest-free loans for indigent Nigerians to fund higher education.
This provision of loans to higher education students is part of Mr Tinubu's reforms for education as contained in his 'Renewed Hope' manifesto.
Allocation not sufficient--lawmaker
The Chairman of the Committee, Teseer Ugbor, in his speech, expressed reservations on the Student Loan Act signed in June, noting that it is unclear if the statutory provision of one per cent of government revenue is sufficient to fund the scheme.
He stated that the House will consider amendments to the existing Act to increase the allocation to three per cent.
"I want to suggest that if there is the need to increase the requirement of one per cent to three per cent. We are ever willing to look at it," Mr Ugbor said.
