Despite high hopes that the troubled and much-maligned appropriations process could return to regular order this year, lawmakers and key aides are already conceding that finishing the 12 annual spending bills by Sept. 30 is a long shot.

“I can’t see that,— Sen. Tom Harkin (D-Iowa), a senior appropriator, said last week. “Hopefully we’ll get them all done before we get out of here by Christmas.—

Buoyed by expanded Democratic majorities and the election of President Barack Obama, House Appropriations Chairman David Obey (D-Wis.) and his new counterpart, Sen. Daniel Inouye (D-Hawaii), earlier this year called for an end to the string of continuing resolutions and omnibus spending measures that have funded the federal government for much of the past 15 years.

Obey set a particularly aggressive schedule for the House last month, when he called for passing all 12 bills individually before the August recess. This week, no less than six markups are scheduled at the full committee and subcommittee level, coming on the heels of last Thursday’s subcommittee markup of the Commerce, Justice and science bill — the first of the year.

But aides say the plans for a quick finish could slip, especially as lawmakers grapple with untangling the increasingly knotty war supplemental bill and an ever-growing policy agenda that includes health care and global warming legislation.

House Democrats had hoped to finalize the nearly $100 billion supplemental bill Friday, but it was stalled over language restricting Guantánamo Bay detainee transfers, funding for the International Monetary Fund and exemptions from the Freedom of Information Act for prisoner abuse photos.

Democrats, who are also weighing the possible last-minute addition of billions of dollars for flu response and “cash-for-clunkers— provisions, are now scrambling to win liberal support for a possible floor vote later this week.

Once the supplemental is put to bed, aides said, it’s still entirely feasible for the House to complete the spending bills before the end of the fiscal year on Sept. 30. But whether the Senate can match that remains an open question.

Senate Majority Leader Harry Reid (D-Nev.) last week laid out the modest goal of completing the legislative branch and Homeland Security spending bills before the July Fourth recess. In an e-mail, a Reid spokeswoman said Democrats hope to finish the rest before October.

Sen. Ben Nelson (D-Neb.), who chairs the Appropriations Subcommittee on the Legislative Branch, last week said he too hopes for a smooth transition back to regular order for the spending bills. “I think this is the way to do the business of the Senate,— he said.

But a crowded agenda could complicate matters as well.

Harkin, who chairs the Appropriations Subcommittee on Labor, Health and Human Services, and Education, laughed when asked about the Labor-HHS spending bill.

“I’m up to my eyeballs in health care reform right now,— he said. A July subcommittee markup is likely for Labor-HHS, but Harkin predicted floor time would be tight.

“This health care thing is going to consume a lot of energy around here, a lot of focus, in July,— he said.

That would leave scant time for completing the spending bills and conferences by Sept. 30, raising the prospect of a continuing resolution of at least a few months, Harkin said.

Inouye last week acknowledged the uphill task he faces. “It’s going to be a challenge, but we’re going to do our best,— he said in an interview. However, he said he would not begrudge losing floor time to the health care debate. “Health legislation is not a daily affair here,— he said.

Another unknown is how cooperative Republicans will be in passing spending bills. Rep. Jerry Lewis (Calif.) and other GOP appropriators last week called the $64 billion in the Commerce, Justice and Science appropriations bill “unsustainable,— but joined Democrats in passing the measure by voice vote.

But it may be a different story in the Senate.

“We’re just going to have to deal with that,— Nelson said. “My hope would be that the other side will not fall in line with their colleagues who obstructed, that they would step aside for the good of the process, the good of the country.—