Charter school advocates are dismayed that some charters may have a tough time tapping funds from the $10 billion Education Jobs Fund, which is meant to help stave off teacher layoffs.

The issue? It’s very complicated, but basically, it comes down to the fact that in some districts and states, some charter school teachers are employees of a charter management organization or an educational management organization, not a school district.

“There’s a lot of head scratching,” said Brooks Garber, the vice president for federal advocacy at the National Alliance for Public Charter Schools. He said that over 1,000 charters contract with management organizations, so a “large number of kids” could potentially be effected. (Check here for the Alliance’s taken the guidance.)

For instance, in Michigan, 80 percent of charter schools contract with management organizations, particularly for human resources purposes (i.e. hiring teachers and other employees to work directly with students.) Under updated guidance released by the Department of Education on Sept. 1, those charters wouldn’t be able to use the edujobs funds to pay teachers that are technically employees of the management organization, but work as teachers in charter schools.

It’s important to note that the guidance doesn’t apply to all charter schools. Charters that are considered their own district are eligible for the jobs funding, and can use it in the same way that school districts can (to pay employees, provide benefits, or hire new teachers.) And charters that are part of another district also can receive the funds, and use the money the same way other schools in the district can.

Also, charters that don’t have any of their own employees (including those who contract with a charter management organization) could use the money to hire new employees. That basically could mean a charter that gets most of its employees through a management organization could technically “hire” a teacher it already has on staff.

But that worries advocates who keep a watchful eye on charter automony, including Gary G. Naeyaert, a spokesman for the Michigan Association of Public School Academies.

“If that’s the bitter pill we have to swallow to use the money, some schools will and some schools won’t,” he said. He says that hiring teachers that are usually contracted through a management organization would force charter schools in Michigan to put that employee in the state’s “bloated” pension system, for instance, which some charters would prefer not to do.

Naeyaert says he doesn’t understand why the guidance can’t be revised so that charter teachers who work for a management organization are eligible for the funds. The guidance goes against the “spirit” of the law, he said.

“These are people who touch kids every day and they should be eligible,” he said.

And Michigan charters aren’t the only ones worried about a potential lack of federal funding. It looks like schools in Connecticut may be in somewhat similar straits.