With the House and Senate now fully engaged in the health care debate, other big-ticket items have fallen by the wayside, which will force lawmakers to cut last-minute deals to keep the government operating and key programs afloat.

The end of September marks a critical moment in this year’s legislative calendar. In addition to being the end of the fiscal year, both the highway and Federal Aviation Administration authorization bills need to either be extended or reauthorized by Oct. 1.

Other policy issues — including the annual debt ceiling — are also on the back burner at this point, while climate change legislation, immigration reform and financial regulatory reform are likely to be formally declared dead for the year by month’s end.

Republicans and Democrats alike said that the intense focus on health care and the fact that it has dragged out for months has hurt Congress’ ability to hammer out agreements on virtually every other major piece of legislation.

“It sure has— made things more difficult, Senate Environment and Public Works ranking member James Inhofe (R-Okla.) said Wednesday. Inhofe and Chairman Barbara Boxer (D-Calif.) are in charge of dealing with the multibillion-dollar highway bill, which is set to expire Sept. 30.

House Transportation and Infrastructure Chairman James Oberstar (D-Minn.) has been pushing for a short-term extension of the highway bill in order to keep pressure on his fellow lawmakers to pass a bill next year.

But Inhofe, Boxer and the White House have rejected that idea, calling instead for an 18-month extension of current law. According to lawmakers close to the discussions, those players believe they can’t move the measure any sooner since health care reform is dominating the debate this year and an election year is around the corner.

Despite the delays, Inhofe on Wednesday said he is confident an 18-month extension will ultimately be adopted, noting that Senate Majority Leader Harry Reid (D-Nev.) is on board.

“Sen. Reid has agreed to do this. … I think he’s committed, and it’s going to get done,— Inhofe said.

Republican and Democratic aides said a similar long-term extension on the FAA authorization bill is also expected.

A senior Democratic leadership aide said Wednesday that Democratic leaders have only now begun preliminary discussions of what this year’s continuing resolution — to keep the government operating beyond Oct. 1 — will look like.

Although Reid and top appropriators are expected to move a one-month CR during the last days of September, no decisions have been made.

Yet to be resolved is how leaders in both chambers will deal long-term with the outstanding appropriations bills. The Senate is expected to stay in session until Christmas, meaning leadership will need to decide in the coming weeks and months whether to continue passing CRs or package the spending measures into an omnibus bill. Most expect leadership to rely on short-term CRs until the end of the year, when Democrats will have to decide how to pass funding for the rest of the fiscal year.

At the same time, lawmakers are facing a looming problem with the debt ceiling, which is expected to be reached next month. The Treasury Department is taking steps to avoid hitting the $12.1 trillion cap, including by shuttering the Supplementary Financing Program set up to help rescue the financial industry. But even if Treasury is able to temporarily avoid the ceiling, lawmakers this fall will likely have to find a way to make further cuts to spending or raise the cap, which would result in a major political fight.

Although Treasury and the House and Senate committees of jurisdiction have been working on the issue, it has largely gone unnoticed by most lawmakers, thanks in large part to the health care fight.