PORTLAND – Maine stands to wind up empty-handed from an eleventh-hour measure approved by Congress to fix a federal funding shortfall in a Medicaid-related health insurance program for poor children.

As a result, the state will have to make up an estimated $6.5 million shortfall or put 3,250 children at risk of losing their coverage next summer.

“There is no help at all,” said Elinor Goldberg, president of the Maine Children’s Alliance. “I think it’s a terrible solution. They negotiated and negotiated and negotiated and came up with no help available.”

About 14,800 children and pregnant women in Maine are served by the State Children’s Health Insurance Program.

Created in 1997, the national program has become too popular for the $5 billion that Congress spends on it each year. As a result, Maine and 16 other states face funding shortfalls.

To address the problem, Congress agreed to shift an estimated $218.7 million that states hadn’t spent from 2004 and 2005 to the states with shortfalls, according to a report by the nonpartisan Center on Budget and Policy Priorities. Full funding to all states would have cost another $815.7 million.

Maine stands to miss out because funds will be distributed in the order in which states will run out of money. In Maine, that isn’t expected to happen until June.

Sen. Olympia Snowe had sought elimination of the shortfall and pledged to continue the fight next year.

“We cannot afford to lose ground on coverage for children,” Snowe said.

Program advocates expressed disappointment that Congress had set a cap of $20 million on the amount that any state had to return in order for the money to be redistributed, even though some states had much more money that had not been spent.