Less than 24 hours before the D.C. Council’s final vote on the fiscal 2013 budget, funding for part of the $3,000 per-student charter school facilities allowance is looking a little wobbly.

The District is negotiating with the U.S. Department of Education over the appropriate use of so-called “three-sector” money. This is the annual federal payment intended to support the D.C. voucher program, charters and DCPS. For the past few years, the District has used a chunk of it to underwrite $200 of the $3,000 per-student allowance. That comes to about $6.5 million a year.

But the Education Department recently informed OSSE that it wanted to restrict use of three-sector money to activities more directly related to raising student achievement. An Education Department official, who asked for anonymity because negotiations were ongoing, said Monday that the department had offered to allow D.C. to use half of the usual $6.5 million for FY 13, but none in subsequent years. The official said OSSE had yet to agree.

OSSE officials had not responded to a request for comment as of 6 p.m.

D.C Council Chairman Kwame R. Brown, who oversees education funding as head of the Committee of the Whole, announced late Monday that he had secured $2 million in non-departmental funds to bolster the allowance. That would still it short of $3,000 per student.

This matters because charter schools depend on steady cash flow from the allowance to pay rent, mortgage and construction loans. Charter educators say lenders get nervous when the allowance fluctuates, making it harder for schools to get financing.

“I am confident that the mayor and his team share my commitment to resolving these critical issues, and I look forward to working with them during the remainder of FY13 and in preparation for the FY14 budget cycle to address the full range of equity concerns for public charter schools, including facilities funding,” Brown said in a statement.

Robert Cane, executive director of the charter lobbying group FOCUS DC, said it was time for the city to find the facilities money on its own and to stop relying on the federal payments.

“I think that in [Education Department] they wonder why the District government can always find money for the school system and not the charter schools,” Cane said.