Gov. David A. Paterson wants to replace the state’s flagship Empire Zone program with a series of new tax credits targeting companies that create jobs and make investments in research and other capital projects.

The governor’s Excelsior Jobs Program would focus on companies in targeted industries, ranging from technology and biotechnology to clean technology, finance and manufacturing.

The new program would have three main elements, all built around tax credits. The backbone of the program will be a tax credit for companies that pledge to create and maintain a set number of new jobs for five years.

The tax credit will be based on a portion of the payroll costs associated with those new jobs, rather than simply the number of jobs being added or retained. “We are evaluating this based on payroll,” said Dennis Mullen, the president and chief executive officer of Empire State Development.

The proposal, which would need approval from the State Legislature to take effect, also includes a research and development tax credit. The tax credit, currently available only to businesses that invest in capital equipment, will be broadened to cover additional types of investment.

A separate investment tax credit also will be available to encourage capital investment. The program would broaden the current investment tax credit, now available to companies investing in manufacturing, production or research and development, to include capital expansion in the state.

“The Empire Zone program has outlived its usefulness,” Paterson said.

A key difference between the Excelsior proposal and the Empire Zone program is that the new program would provide tax credits only after companies have met the job or investment criteria. The Excelsior program also would not target any particular geographic area, as the Empire Zone program does.

“The rewards are post-performance,” Mullen said. “It’s very targeted. It’s built around [research and development].”

The Empire Zone program, which has provided incentives to more than 9,000 New York companies, has been criticized because a significant number of companies receiving benefits failed to meet their promised investment and job creation targets.

Paterson also called for a series of other economic development initiatives, ranging from the creation of a $25 million seed fund for technology ventures that are spawned by research conducted at the state’s colleges and universities, to programs to promote energy efficiency and encourage the reuse of abandoned factories.

“I think there were a lot of positive and encouraging initiatives,” said Brian McMahon, the executive director of the New York State Economic Development Council. “We’re particularly encouraged by his focus on the innovation economy.”

Andrew J. Rudnick, the president of the Buffalo Niagara Partnership, said the Excelsior program is a step in the right direction. “They’re moving away from place-based incentives to incentives that will encourage new jobs and investment,” he said.

Both McMahon and Rudnick, however, said further details were needed to fully evaluate the proposals. McMahon said he had concerns that the Excelsior program would offer sufficient help for existing businesses, especially given the state’s high taxes and burdensome regulations.

“We need significant and robust economic development incentives to overcome those costs,” McMahon said. “It certainly appears that the level of incentives in the Excelsior program are significantly lower than they are in the Empire Zone program.”

Rudnick also voiced concerns that the amount of funding available under the Excelsior program would limit its effectiveness. “That’s the harsh reality of trying to do something like this with the financial condition the state is in,” he said.

Kenneth Adams, the president of the Business Council of New York State, said the group supports the creation of a replacement program for the controversial Empire Zone initiative. But he said the Excelsior plan falls short in supporting new capital investment and job retention.

“In addition to using job creation as a criteria for tax credits, significant capital investment by in-state companies that helps them become more competitive and retain jobs in the state should also be a component of the program,” Adams said.

Companies currently participating in the Empire Zone program will not lose any of the incentives for the duration of the scheduled period, which can run for up to 10 years, Mullen said.

Allison Duwe, executive director of the Coalition for Economic Justice, said the elimination of the Empire Zone program “will save New York’s taxpayers $600 million at a time of crisis when every penny counts.” She also urged state officials to implement reforms at the state’s industrial development agencies.

Other elements of Paterson’s economic development proposals include:

The creation of a Manufacturing Legacy Program to take an inventory of available manufacturing sites and market those locations for re-use in a way that melds with regional economic strengths.

Submitting legislation for an eight-year extension to the New York Power Authority’s Power for Jobs program, which offers 400 megawatts of low-cost electricity to businesses. The program, which has received several short-term extensions in recent years, is set to expire in late May.

Focusing economic development efforts upstate on ways to “make upstate New York the preferred back office for corporate America,” Paterson said.

Mullen said state officials hope the back-office initiative will be able to build upon ties to financial institutions that already have extensive operations in New York City.

The establishment of a revolving loan fund for small businesses, targeting minorities, women and other disadvantaged groups that have trouble obtaining conventional financing.