Universities are talking to government officials about where exactly the cuts will fall
England's universities warn budget cuts will be "challenging" and say efforts to limit their damage will be needed.
The Chancellor has announced that £600m will be "saved" by 2012/13 from across "higher education, science and research budgets, including student support".
Bodies representing university leaders say the sector is already absorbing considerable "efficiency savings".
But ministers point to a 25% real term increase in funding in higher education since 1997.
In the pre-budget report, the Chancellor Alastair Darling said there would be cuts of: "£600 million from higher education and science and research budgets from a combination of changes to student support within existing arrangements; efficiency savings and prioritisation across universities, science and research; some switching of modes of study in higher education; and reductions in budgets that do not support student participation".
It is not yet clear where precisely the cuts will be made. Ministers say decisions will be taken after they receive a report from a review on university funding due in the autumn.
Earlier this year the government asked universities to find £180m in efficiency savings by 2011.
Professor Steve Smith, president of umbrella body Universities UK, said: "The university sector has provided an excellent return on the last 12 years of public investment.
"However, the sector is already absorbing considerable efficiency savings and the announcement that by 2012-2013, £600 million will be cut from higher education and science and research budgets will be extremely challenging for universities."
He said Universities UK would work closely with the government and England's university funding funding body, Hefce, "to work through how the cuts will fall and cause least damage".
University funding review
Universities UK said the cuts made current discussions about the future funding of higher education even more urgent.
Professor Smith said: "It is therefore essential that we review student support costs as part of the Browne Review."
The Browne Review was commissioned by the government to look at the future of higher education funding, and the student tuition fees and support system. It is due to report next autumn.
A spokeswoman for the Department for Business, Industry and Skills said: "Higher education has seen a 25% real term increase in government funding since 1997 but in this difficult fiscal climate we need to focus spending tightly".
Alice Hynes, chief executive officer for GuildHE, which represents some universities and colleges, said: "The delivery by higher education is one of the decade's success stories and the government has begun to recognise the complex connections between economic growth, education, innovation and entrepreneurial skills.
"It must be cautious what risks it takes with this dynamic sector if it makes higher education the target of sharp cuts.
"The requirement to make £600 million savings by 2012/13 from budgets... will be severely demanding. GuildHE members will work with their UUK colleagues and Hefce to look at ways to achieve outcomes which create the least damage, while maintaining the longer term health of the higher education sector.
"The government must continue to recognise the significant role that all of higher education plays in delivering a skilled workforce that can engage in industries and professions that will take us out of recession and keep our place on the world stage."
In the Commons on Thursday, Higher Education Minister David Lammy said the cuts would amount to 4% to 5% of the government spend on higher education, science and research.
This was "reasonable" compared with how hard the downturn had affected people.
The government, he said, was "committed to the higher education system and continuing to pay a significant share of the cost of educating each student but we are in a difficult climate".
Once ministers had received the review report on higher education funding and student finance next summer, the necessary decisions would be taken on "where and how these savings can best be made".
It was right that higher education institutions, which had benefited significantly from extra funding in recent years, should recognise the contribution they had to make at this time, he added.