Virginia’s ambitious program to compensate teachers based on performance has encountered its first hurdle: Only 6 percent of eligible schools have elected to participate.

Gov. Robert F. McDonnell (R) announced in April that the state would allocate $3 million for teacher bonuses in “hard-to-staff” schools as a way to recruit and retain top instructors in challenging classrooms. The one-year program is due to begin in the coming academic year.

But the overwhelming majority of Virginia school districts declined the governor’s invitation, citing concerns about the criteria used to judge teachers, the sustainability of the initiative and the accelerated implementation timeline.

Those concerns speak to the challenges facing a key item on President Obama’s education reform to-do list, now hotly debated by school boards and legislatures.

Virginia officials say that they didn’t expect all of the 169 eligible schools to participate in the program and that the low participation rate doesn’t preclude success. Ten schools from seven districts — none of them in Northern Virginia — have applied for the funds.

The participating schools are in Dinwiddie, Goochland, Accomack, Caroline, Patrick and Greensville counties and Roanoke City.

“There’s no point in pretending that there aren’t different views on performance pay, and it’s clear that some local school boards felt this would not help them fit a need,” said Charles Pyle, spokesman for the state Department of Education. “We’re pleased with the list. . . . We have school divisions participating that have real staffing problems.”

Officials in the education department and the governor’s office say the initiative will continue as planned and that the $3 million pool will not be diminished. Unused money will be returned to the state’s general fund.

“Over time, as more people hear about the success of the 10 schools participating, we expect support for the program to increase,” said McDonnell spokesman Jeff Caldwell.

The initiative will use a newly created metric to measure teacher performance based largely on student progress on standardized tests. The metric also takes into account professional knowledge, instructional planning and professionalism, as well as other criteria.

Florida, Ohio, Georgia and a number of other states are mulling performance-pay initiatives, despite opposition from teachers unions. Some states have crafted such programs in an effort to secure funds from the Obama administration’s Race to the Top initiative.

“The opposition is usually in response to the criteria being used, not the idea of performance pay,” said Matthew Springer, director of Vanderbilt University’s National Center on Performance Initiatives. Programs in states where teachers helped craft program guidelines, he said, such as Minnesota and Texas, have been both successful and popular.

But the Virginia Education Association, the state’s largest teachers union, objects to both the specific criteria being used as well as the fundamental principle underlying merit pay.

“The assumption is that teachers are holding back their best work because they’re not being paid enough,” said Kitty Boitnott, the association’s president. “It’s insulting to professionals, yet politicians are completely taken with it.”

Some districts, such as Fairfax, cited failed efforts to introduce merit pay over the past several decades as a reason for declining state funds.

“We are not planning to apply for any pay-for-performance grants,” Fairfax Superintendent Jack D. Dale told The Post in April. “We previously had a performance-pay system in Fairfax that was ultimately not successful.”

Officials from other districts said that schools categorized as “hard to staff” did not suffer from staffing problems and would gain little by implementing performance pay.

Several districts, such as Prince William County, are already participating in other performance-pay initiatives, including the federal School Improvement Grant program. Implementing more than one performance-pay program simultaneously would be logistically impossible, officials said.

Prince William will launch an $11.1 million merit-pay program next year in its 30 poorest schools, but that initiative will allocate awards based on the overall performance of schools, not individual teachers. Such programs tend to garner more support, particularly among teachers, experts say.