Senate Republicans are warning Governor Spitzer that Albany won’t be able to afford what it would cost to adopt the recommendations made by his higher education commission.

Mr. Spitzer, whose administration is incorporating a number of the commission’s policy prescriptions into next year’s budget, has praised its preliminary report as a roadmap for delivering on his campaign promise to transform New York’s public universities into an elite institution.

Republicans are signaling they will refuse to fund the commission’s plan unless the governor meets their budget demands in other areas, including education spending, health care, and property tax cuts. Senate officials also say the commission may be underestimating the cost of its proposed initiatives.

“That’s a lot of spending with no way to pay for it,” a spokesman for the Senate Republicans, John McArdle, said. “It begs the question: What programs is he going to cut, and what taxes is he going to raise to pay for it?”

The first-year cost to Albany of implementing the recommendations in the report is estimated to be at least $750 million, according to the Senate budget office.

A proposed “compact” between the public university systems and Albany — under which the state agrees to cover 100% of mandatory costs such as labor contracts and energy and assume 20% of costs of new academic initiatives — is expected to cost Albany more than $3 billion over five years.

On top of that is a proposed “innovation fund” for providing grants for research in the physical sciences, bioscience, engineering, and medicine at the State University of New York, the City University of New York, and private New York universities, which comes with a price tag of $3 billion over 10 years.

The report also calls on Albany to empty a backlog of $5.8 billion in capital maintenance projects over the next five years.

Senate officials say hiring an additional 2,000 full-time faculty members, including 250 senior research academics working in $1 million labs, would cost state government substantially more money than allotted for in the compact outlined in the 85-page report, which was released on Monday.

Commission officials insisted their dollar estimates are accurate. The executive director of the panel, John Reid, said they “tried to be prudent” in their proposals. “If you look at the data, you could easily justify more full-time faculty than we recommended,” he said.

As Mr. Spitzer heads into his second year, his administration is grappling with a growing list of spending obligations and promises amid economic uncertainty.

Next year’s deficit stands at $4.3 billion, a figure that could grow or shrink by a wide degree, depending on end-of-year economic indicators, such as Wall Street bonus payments.

Republicans, who have been engaged in a bitter feud with the governor for much of the year, are unlikely to hand Mr. Spitzer any easy victories, and may use their resistance to the higher education plan as leverage over other priorities of the administration.

Mr. Spitzer has vowed not to raise taxes, but he has also said he is committed to a four-year plan of increasing public school aid by $7 billion.

The governor has also pledged a $2.5 billion expansion of the state-funded School Tax Relief program by 2010.

Meanwhile, the governor, who is in the process of drafting a universal health care program, will face tremendous political pressure to spare the hospital industry from significant budget cuts.

A spokeswoman for the governor, Christine Anderson, yesterday said the administration shares some of the concerns of the Republicans regarding the commission’s report.

“The governor has said he’s evaluating the proposals and their economic feasibility,” she said. “It’s all about choosing priorities.”

While Republicans are questioning how New York would be able to afford a surge in new higher education money, Democrats in Albany are opposing a key recommended source of new revenue to pay for it.

Assembly Democrats say they object to the proposed automatic tuition increases of 2.5% to 4% a year, labeling it a tax on the middle class.

Assemblyman Richard Brodsky, a Democrat of Westchester, said tuition hikes would fit a pattern he said the governor has set of hiking fees to raise revenue.

“As best I can tell, Eliot Spitzer believes in user fees that hit the middle class,” he said. “It’s congestion pricing fees. It’s tolls. It’s tuition increases. They hit the middle class and let the rich escape.”

A senior adviser to the governor, Lloyd Constantine, who helped oversee the higher education commission, said the governor “has yet to embrace any particular part” of the report.

“I don’t think either the governor or the Legislature will embrace the entirety of this,” he said. “From this, will emerge important initiatives this year that will be embraced by the governor and by both houses.”

The commission is scheduled to produce a final report in June.