The cuts in existing and planned jobs - the first in the hospital's 30-year history - would be forced by the loss of a $55 million state subsidy the teaching hospital receives as part of the State University of New York system.
"The reason we say the sky is falling is because it is a critical part of our budget. There is no way we can sustain these cuts without laying people off," Dr. Steven Strongwater, the hospital's chief executive said in an interview.
The three hospitals in the SUNY system lose a combined $135 million in direct state aid in the proposed budget.
That's on top of anticipated revenue losses caused by redesign of the state's Medicaid program, the state-federal insurance plan for low-income and disabled people. Those changes will impact nearly all hospitals and health care providers.
Strongwater said he would shutter entire programs rather than order across-the-board layoffs. He declined to say which programs would close.
Layoffs would affect employees ranging from top executives to nurses to maintenance workers, he said.
If 700 jobs were cut, as many as 500 would involve existing employees, said hospital spokeswoman Lauren Sheprow.
Jeffrey Gordon, a spokesman for the state budget office, said Cuomo "is seeking to minimize layoffs by working cooperatively with employee unions to reduce costs."
Stony Brook hospital has 5,500 workers and an operating budget of $880 million. Over the past decade, the hospital has added 1,500 jobs.
Last year, the hospital offered employees early retirement packages but overall staffing was not reduced.
The hospital's largest unions say the cuts would damage the Island's health care system, leaving many residents without critical services. Stony Brook has the only burn unit, psychiatric emergency room and Level 1 trauma center on Eastern Long Island.
"The membership is in a panic state. These people are just trying to make a living," said Carlos Speight, president of Civil Service Employees Association Local 614. The union represents 2,800 workers, including nursing assistants, clerks and engineers.
The union's current contract expires at the end of March, said Speight, who was in Albany Tuesday speaking with legislators.
"If the state pushes the hospital over the cliff, they're going to drag the medical school down, too. That is a big concern," said Philip Smith, president of United University Professions, which represents more than 3,600 professionals, including doctors, nurse supervisors, clinical researchers and academics.
If 700 jobs are eliminated at the hospital, hundreds more would be lost in the region, said Pearl Kamer, chief economist for the Long Island Association, a business and civic group.
For every 10 hospital layoffs, seven non-hospital jobs are lost, said Kamer, citing a U.S. Bureau of Economic Analysis formula.
"Whenever you see an employment loss, we know that there's a ripple effect," she said.