Wealthy undergraduates in England will be better off while women, disadvantaged students and those from the north and Midlands are most likely to be worse off under proposed changes to student finance, according to the government’s own analysis.

After the official announcement of an overhaul of how graduates in England will repay tuition fee and maintenance loans in the future, ministers also urged universities to make “efficiencies” to cope with the reduced income they faced from a prolonged freeze on tuition fees.

The changes would result in students who enrol in 2023-24 having to make repayments for 40 years rather than 30 under the student loan system that has been in place since 2012.

Save the Children labelled the reforms as “among the most regressive yet”, while the Institute for Fiscal Studies said that high-earning borrowers “stand to benefit substantially”.

According to the IFS, graduates on lower-middle earnings would suffer the biggest proportionate loss, the equivalent of more than a penny in every pound they will ever earn during their lifetime.

Middle and lower income graduates would also be hit by the government’s move to lower the repayment threshold from its current rate of £27,000 to £25,000 as the point at which graduates must use 9% of their income to repay loans.

An equality analysis on the proposals by the Department for Education, states that “those likely to see some negative impact with increased lifetime repayments under the reforms” include younger and female graduates as well as graduates “from disadvantaged backgrounds, or reside in the north, Midlands, south-west or Yorkshire and the Humber”.

The analysis shows that the lifetime repayments of a graduate in 2023-24, earning £22,000 in current prices with projected lifetime earnings of £850,000, would rise by 150% – from just below £9,700 now to £24,000.

In contrast, the loan repayments of a graduate in the top 10% of earnings with an annual pay of £88,000, who would enjoy lifetime earnings of £3.5m, would drop from £53,000 to £39,000.

Wealthy graduates particularly benefit from the government’s decision to stop charging higher earners an extra 3% interest rate. The changes will set interest at the rate of inflation, which the universities minister Michelle Donelan hailed as “injecting fairness into the system”.

The IFS’s analysis said the changes would substantially increase the proportion who pay off their student loans, which now average close to £50,000. Students from a wealthier background tend to have lower borrowings as the amount of maintenance loan is linked to parental income. Whereas only a quarter of graduates are expected to have repaid their loans in full within 30 years of graduation, under the new system 60% can be expected to.

“The long-run benefit for the taxpayer will be modest at around £1bn per cohort of university entrants, as higher repayments by borrowers with low or middling earnings will be mostly offset by lower repayments of high-earning borrowers,” the IFS said.

On top of higher repayments, the institutions at which students study will receive less in real terms. Donelan confirmed that tuition fees will remain frozen for a further two years, at no more than £9,250 for English universities, meaning an effective cut after inflation.

“We’re asking everybody to share this balance, and we want to continue to drive the sector to find efficiencies. There are more efficiencies that can be found and it is important that students get value for money for their degree,” Donelan said.

The government is to commit an extra £900m over three years, including £750m for teaching targeted at science, technology, medicine and other high priority subjects. But the Russell Group of research universities said inflation meant the extra grant would not be enough to compensate for the cost of such courses.

The Department for Education also published a controversial consultation to restrict numbers on certain courses, and set minimum criteria for school leavers to qualify for student loans, such as requiring at least a grade 4 in GCSE maths and English.

Martin McLean, of the National Deaf Children’s Society, said: “This misguided proposal would make it even harder for deaf young people to reach higher education and it must not go ahead.”

The government also announced that a consultation on shifting the university admissions process until after A-level results had been dropped because it was too complex.