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The federal government is being accused of dodging promised reforms to bring down soaring university fees, after rejecting efforts to have them scrutinised by a new watchdog.

On Monday, legislation to establish the independent Australian Tertiary Education Commission (Atec) passed the Senate with a number of amendments, including to improve its resourcing and ensuring it had a focus on research.

But Labor refused to support a Greens amendment that would require Atec to prepare reports and advise the education minister on the student fees charged for each subject, which would include tackling the Morrison-era Job-Ready Graduates (JRG) package.

The JRG scheme was introduced in 2021, and led to arts degrees costing students more than $50,000 – while other degrees including in science and mathematics had fees slashed by up to 59%.

The education minister, Jason Clare, has repeatedly deferred any JRG reforms to the Atec.

Asked about the “failed” JRG price signals for humanities students at the AFR higher education summit in August, Clare said Atec would do the “heavy lifting to design a system where the funding follows the student and reflects the actual cost of the degree”.

The Atecs’s establishment had already been delayed, after the government initially committed to it being formally up and running by January.

The head of Universities Australia, Luke Sheehy, said providers had “always supported” the Atec but that it was disappointing that a “key piece” was missing.

“It leaves a critical gap in the Atec’s remit and sends a clear signal that the government is not yet prepared to fix the Job-Ready Graduates package,” Sheehy said.

“JRG is punishing students with $50,000+ degrees and ripping close to a billion dollars a year out of universities.”

The legislation allows Atec to provide advice to the government on commonwealth funding to universities, but it is not required to consider student contributions and makes no explicit mention of JRG.

Sheehy said without addressing student contributions, “we risk entrenching the very funding challenges the sector is trying to solve”.

Experts and the government have conceded JRG – designed to incentivise students into Stem (science, technology, engineering, and mathematics) courses – has instead discouraged students from lower socioeconomic backgrounds from attending university.

New university enrolments from students with low socioeconomic backgrounds dropped by 10% between 2020 and 2024, according to data analysis by Innovative Research Universities (IRU).

IRU’s chair and the vice-chancellor of Western Sydney University, Prof George Williams, said he was also “disappointed” reforming JRG had been excluded from Atec’s responsibilities and it should be an “urgent priority” for government.

Clare told Guardian Australia he had “been clear” JRG had failed, as outlined in the Universities Accord, which warned it needed “urgent remediation” when it was handed down to Labor in early 2024.

“We’ve bitten off a big chunk of [the accord’s] recommendations already – 31 of 47 in full or in part,” Clare said.

“The next step is what we are doing to make university quicker and cheaper … by cutting the length of your degree if you already have a Tafe qualification in the same area.

“That’s what I have asked the Atec to drive this year. There’s a lot to do. It’s like eating an elephant. You have to do it one bite at a time.”

The Greens’ spokesperson for higher education, Mehreen Faruqi, said Labor had “railed against the JRG bill in opposition”.

“Yet after four years in power, the government has passed another higher education bill that fails to overturn this trainwreck of a policy,” she said.

“To establish the Atec without any reference to Job-Ready Graduates and repealing fee hikes is again kicking the can down the road, while students and young people suffer under the weight of massive fees and crushing debt.”