Connecticut hospitals are likely to get much less state and federal aid than they expected this year, but the losses won’t be as great as they feared after Gov. Dannel P. Malloy slashed the state budget in September.

Under the latest budget deal passed by the Legislature and awaiting Malloy’s approval, hospitals will get a combined $164.3 million in state and federal funds, up from the $64 million they would have received under the governor’s September plan.

But that figure is far short of the $255.9 million hospitals stood to gain from the original budget, and many hospital officials are scrambling to figure out how they’ll make do with so much less. Worse, the cuts come after several years of rising taxes and falling state aid that have already forced many hospitals to squeeze staff and services.

“We’ve had reductions in staff, we’ve made benefit changes, frozen pensions and sold services,” said Steven Rosenberg, the chief financial officer for the Western Connecticut Health Network, which includes Danbury, New Milford and Norwalk hospitals. “The problem is we’re running out of things to cut that won’t impact quality and our ability to provide the kinds of services we want.”

Rosenberg said the system has been cutting staff for three years and earlier sold its dialysis and retail pharmacy services and outsourced its dietary department.

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Danbury and New Milford hospitals were slated to receive about $10 million under this year’s original budget, and would have lost all but $2.5 million under the September cuts. According to data from the state Office of Policy and Management, the hospitals can now expect to get $6.2 million.

“We’ve made progress, but we need to make more,” said network spokeswoman Andrea Rynn. “This is not a problem that’s going away with the latest give-backs. At the end of the day, these numbers are so critical only because they represent people.’

Connecticut has long provided direct aid to hospitals. In 2012, however, the state began taxing hospitals and returning the proceeds as way of drawing down federal matching grants. At first, the money returned to the hospitals exceeded the taxes paid, but in recent years, the balance has flipped, and the hospitals are paying more than they get back from the state.

In 2012, state hospitals received about $400 million in state and federal funds while paying about $350 million in taxes, said Stephen Frayne, the senior vice president of health policy at the Connecticut Hospital Association. But this year, hospitals are projected to owe $556.1 million in taxes but receive only the $164.3 million provided in the recent legislation.

Hospitals said they have struggled to find ways of saving money to deal with this shift.

In September, before the governor’s proposed cuts, Stamford hospital administrators had already announced a plan to lay off 20 employees, leave more than 100 vacant positions unfilled and make cuts in community outreach programming.

“We appreciate that the legislators acknowledged the burden placed on community hospitals and helped restore some of the unanticipated additional cuts to Medicaid reimbursements, but we still need to address the longer-term impact of burdensome taxes on the hospitals that are responsible for caring for our communities,” said hospital spokesman Craig Andrews.

Officials at Greenwich and Bridgeport hospitals, which are part of the Yale-New Haven Health System, said they have so far found ways to save money without cutting staff. But if the hospitals continue to face millions in tax bills, services are certain to suffer, said Dana Marnane, the health system’s spokeswoman.

“We can’t continue to balance the state budget on the backs of the hospitals,” Marnane said.

Malloy spokesman Devon Puglia said Tuesday the governor hadn’t received the legislation and declined to comment further on the issue.

Frayne said the hospital association is grateful for the Legislature’s budget deal, but added that something has to give.

“We keep finding ourselves in a loop that keeps repeating itself,” he said. “A proposal comes from the administration to have fairly significant cuts to the hospitals, then the Legislature comes in and mitigates the cuts, but there’s a cut nonetheless.

“While clearly it’s a better place than without the relief, it’s still worse than where we’ve started,” he said. “That’s not progress.”