Hundreds of top-rated upstate science and math teachers will be eligible for $15,000 in annual stipends under a new mentorship program announced by Gov. Andrew Cuomo this afternoon.

New York City teachers aren’t eligible for the stipends, in part because they still lack an evaluation system to identify them according to a four-tiered ratings scale. But the state is relying heavily on a highly-regarded city-based mentoring organization to implement the program in selected higher education institutions.

Under Cuomo’s “Master Teacher Program,” 250 teachers from schools located in four upstate regions — North Country, Mid-Hudson, Central New York and Western New York — will be selected to receive a total of $60,000 in extra pay over four years. In exchange, the teachers will be trained at State University of New York education colleges and tasked with mentoring new teachers in the science and math subjects.

Recruiting and rewarding top teachers to work in high-demand subject areas was one of the recommendations put forth by Cuomo’s Education Reform Commission last year. Cuomo also secured $11 million in the 2013-2014 state budget to develop the program, which is scheduled to expand to more districts.

“As part of the state’s work to transform our education system and put students first, we are committed to investing in great teachers to educate our students and create a highly-trained workforce to drive our future economy,” Cuomo said in a statement. “This program will reward those teachers who work harder to make the difference and whose students perform better as a result.”

Only middle and high school math and science teachers can submit applications, which will be available starting on July 1. They also must have at least four years of experience and receive “highly effective” ratings on their 2012-2103 evaluations in order to qualify for the stipend.

Teachers in New York City, the only district in the state without a teacher evaluation system in place this year, aren’t eligible to apply for the stipends.

The program is getting a big boost from a New York City-based mentorship program, Math for America, whose model is being adopted at four upstate SUNY schools — Plattsburgh, Buffalo State, New Paltz and Cortland.

The SUNY schools will also rely on Math for America’s staff to help train the initial cohort of master teachers, and develop the curriculum that will be used for future cohorts. Eventually — and if the program receives funding in future state budgets — training will be entirely turned over to the higher education institutions.

The stipend program is different from a “merit pay” system, which are controversial with teachers unions because of concerns that it breeds unhealthy competition by pitting one teacher against another. Research has also shown that students do not learn more when given teachers who are paid for performance.

Instead, the stipends are meant to recognize top teachers and compensate them for work beyond their normal schoolday  responsibilities.