(NBC NEWS) -- Federal government officials told agencies to begin executing plans for a partial government shutdown Monday as Congress failed to reach an agreement on a funding measure.

In a memo to executive branch officers sent less than half an hour before a midnight deadline, Office of Management and Budget director Sylvia Burwell said there was no "clear indication" that Congress would reach an agreement to keep the government's lights on by 12:01 a.m. ET

"Agencies should now execute plans for an orderly shutdown due to the absence of appropriations," she wrote. "We urge Congress to act quickly to pass a Continuing Resolution to provide a short-term bridge that ensures sufficient time to pass a budget for the remainder of the fiscal year, and to restore the operation of critical public services and programs that will be impacted by a lapse in appropriations."

The shutdown is expected to place tens of thousands of federal workers on furlough, close national parks and monuments, and disrupt services like food assistance and IRS audits. Services like benefit payments and national security operations would go on as usual, and – because of a bipartisan measure passed by both houses of Congress and signed into law by the president late Monday – members of the military will continue to be paid.

As the clock ticked down to midnight, the House announced that it would try to shift decision-making to a bipartisan "conference" of lawmakers from both chambers, but Democratic Senate Majority Leader Harry Reid immediately rejected that plan.

"We will not go to conference with a gun to our head," he said.

Due to the time needed for parliamentary procedure, it was clear that the House and Senate would not reach any agreement in time to avert the shutdown.

Less than an hour before the funding deadline, House Republicans were set to formally request a bicameral committee late Monday evening to hash out some middle ground between the Democratic Senate's "clean" government funding bill and the GOP-led House's proposal to delay a key part of Obamacare and nix health care subsidies for congressional staffers.

"It means we're the reasonable, responsible actors trying to keep the process alive as the clock ticks past midnight, despite Washington Democrats' refusal - thus far - to negotiate," the GOP aide said.

After the plan was reported, Reid said the Senate wouldn't "go to conference until we get a clean CR," and accused Republicans of "playing games" at the eleventh hour.

Rep. Chris Van Hollen, D-Md., told reporters the conference plan was simply "a recipe for shutting down the government."

All this comes after the Senate -- for the second time Monday -- rejected a House-passed measure that would have delayed a key provision of Obamacare while funding the government for an additional few weeks.

With just hours to go before the midnight deadline, the Senate swiftly nixed a House-passed government funding proposal late Monday, tossing the legislation back to the lower chamber with unusual speed as the nation careened towards a federal shutdown.

Shortly after receiving the House proposal to fund the government and delay a key provision of the president's health care law, the Senate voted along party lines to send the bill back to the House for a last-ditch effort at meeting a midnight deadline to keep the government's lights on.

Reid said on the Senate floor before the vote that Republicans "have lost their minds" by repeatedly voting for "ridiculous policy riders" destined for failure in the Democratically-controlled Senate.

The House measure -- which would fund the government through mid-December but also delay Obamacare's individual mandate by one year -- passed 228-201, with 12 Republicans bucking their leaders to vote against the plan and nine Democrats voting for it.

Speaking on the House floor shortly before the final vote, House Speaker John Boehner said the vote to delay the mandate was about "fairness."

"I would say to the president: This is not about me," Boehner said. "This is not about Republicans here in Congress. It's about fairness for the American people."

Republicans were not united on a key procedural measure shortly before the final vote on the House plan, prompting some speculation that it would fail and Boehner would be forced back into negotiations. Ultimately only a handful of Republicans broke with Boehner to oppose it.

A bloc of moderate Republicans began speaking out against the measure Monday afternoon, noting that the House's repeated attempts to tie Obamacare changes to the government funding measure had failed in the Senate.

"We've already launched two volleys unsuccessfully and now it's time to go on with the business of governing the country.," Rep. Charlie Dent, R-Pa., told reporters. "The hourglass is already empty and it's time that we pass a clean CR."

And outside conservative groups were split on the newest version of the funding bill. Heritage Action argued that the move to delay the individual mandate does not go far enough, although the group says it will not hold votes of support against Republican members. The anti-tax group Club for Growth urged its members to vote for the new House measure.