AUGUSTA – Programs affecting state government and individual Mainers are in legislative limbo with Congress adjourning and spending bills for most of government dying with the crack of the gavel ending the session.

“The CR [continuing resolution] allows spending at last year’s levels, but that causes problems for the agencies and for programs,” said 1st District Rep. Tom Allen, a Democrat. “Some departments and agencies can’t get the increase in funds that they need to provide the services they are providing.”

He said that in some cases agencies must continue to fund programs at last year’s level, even though the budget legislation under consideration would reduce that spending. Only two budget bills, the one for the Department of Defense and the measure for the Department of Homeland Security, have been approved and signed into law.

Maine Finance Commissioner Rebecca Wyke said the state is getting used to Congress leaving some budget issues unresolved, but, she said, with only the two budget bills adopted it makes what is usually a bad situation worse for the states.

“We have contingencies built into the budget because of the uncertainty there is with federal funding,” Wyke said. “But it does appear to be more challenging this year with more agencies potentially affected.”

Many state departments receive significant federal funding, such as the Department of Environmental Protection, the Labor Department, and the Department of Health and Human Services. Some individual programs, such as the Maine Drug Enforcement Agency, also depend on federal funds.

For example, funding for the State Children’s Health Insurance Program, or SCHIP, is underfunded by $900 million. That is a shortfall of about $6.5 million in Maine, and Gov. John Baldacci estimated that 3,250 children out of the 14,800 on the program would lose coverage.

Wyke said the SCHIP shortfall is one of the many federal budget changes the governor is weighing as he completes the budget proposals state lawmakers will get next month.

“Failure to pass the budget bills have a lot of unintended consequences,” Sen. Susan Collins said. “If we don’t get the budget measures passed quickly, we could see actions like workers having to be furloughed from Social Security offices. These should have been passed before the Congress went home.”

Allen said the Department of Agriculture has not been able to release housing funds as expected because of the lack of a budget.

“Our office alone has heard from about 40 buyers that were left in the lurch because the Department of Agriculture did not have enough money to fund those loans,” he said, “Now that problem is going to get worse.”

Second District Rep. Michael Michaud said that even with the promise by incoming House Speaker Nancy Pelosi to have the House meet five days a week, it will be difficult to reach agreement on all of the budget matters.

“There are going to be members on the Democratic side that are going to want to rewrite a lot of the budget bills,” he said, “Not that they shouldn’t be rewritten, because many should. But that will take longer to do, and that means a lot more time to get budget agreement.”

Michaud said while some Democrats want to make changes in the current year budget, others are urging swift passage of the budget bills. He said there is plenty of time to put the “Democratic stamp” on the new budget measures.

“I think we can get all of the budget bills done this summer,” Michaud said, “before the start of the federal budget year in October.”

Republican Sen. Olympia Snowe was sharply critical of her own party leadership for not keeping Congress in session to pass the budget bills. She said Congress should have met throughout December, if necessary, to pass the budget measures.

“I regret we have not addressed all of these appropriations bills,” she said, “and there is a list that just goes on of legislation that we should have considered and passed.”

Snowe said legislation such as her proposal to allow the secretary of Health and Human Services to negotiate with drug companies for lower prices, funding for the health insurance program that helps poor children, and energy legislation should at least have been considered before lawmakers called it quits for the session.

“We were elected to do the people’s business and we did not get our work done,” she said.

Congress returns in early January and the continuing resolution ends Feb. 15. Wyke said Gov. Baldacci will be submitting his supplemental budget in early January and it likely will need several changes as Congress completes action on budget bills for the current year.