The group of eight colleges in the US known as the Ivy League, are finding it difficult to meet their expenses amid cuts in federal research funding.
Bloomberg reported that at least half of the institutions in the group ran budget deficits in the previous fiscal year. The Ivy League is composed of Brown University, Columbia University, Cornell University, Dartmouth College, Harvard University, Princeton University, the University of Pennsylvania, and Yale University.
Among the schools, Harvard University, Yale University, Cornell University and Dartmouth College reported budget deficits in the year ended in June. Brown University had a budget surplus after it used reserves to fill the gap internally, according to the news agency.
Cambridge, Massachusetts-based Harvard, the world's richest school with a $32.7bn (£20bn, €23.7bn) endowment, last month reported a $33.7m deficit in the year ended in June, up from a $7.9m deficit a year ago.
The second-richest university with a $20.8bn endowment, Connecticut-based Yale, had a $39.2m gap in fiscal 2013 following a surplus last year.
Ithaca, New York-based Cornell University posted a $31m deficit and Hanover, New Hampshire-based Dartmouth College reported the smallest deficit in the group at $1.8m.
Brown University in Rhode Island had a surplus, after it used $5.5m from reserves to balance the fiscal 2013 budget. Meanwhile, Princeton University in New Jersey and Columbia University in New York posted increases in net assets. The University of Pennsylvania in Philadelphia is yet to report its fiscal 2013 results.
"While elite universities are better positioned than most colleges because of their vast wealth and student selectivity, they are striving to contain costs such as employee benefits while maintaining their current levels of student financial aid," Bloomberg wrote.
Sequestration is an austerity measure undertaken by the US federal government, in which the government's spending will be cut automatically in particular categories of outlays.
The automatic spending cuts that came into force earlier this year have affected the elite universities, as they rely heavily on government grants for research purposes.
The universities suffered budget gaps during the credit crisis as they lost a significant portion of their endowment funds, which they use to subsidise their operations.
The recent budget gaps come albeit the institutions' deep spending cuts in order to make up the shortfalls. They are also setting higher fundraising targets to meet their expenses, according to Bloomberg.