A top analyst said as the Pentagon tries to thwart “sequestration” budget reductions it should “take a lesson” from how Congress rushed to make those cuts less onerous on the FAA and the flying public.

President Barack Obama indicated Tuesday that he will sign the bill that House sent him last Friday to give the FAA more flexibility in applying sequestration cuts to reduce the much-publicized recent delays at airports triggered by the furloughing of FAA staff.

Obama told reporters at the White House that he would not veto the FAA bill–even though he has balked at piecemeal solutions to ameliorate the impacts of sequestration on different parts of the federal budget, including the Pentagon. The $1.2 trillion in decade-long sequestration cuts to defense and non-defense spending started March 1. Obama and some lawmakers, particularly Democrats, want to find an alternate plan to replace the cuts, which are designed to be applied across-the-board to agencies budgets.

Todd Harrison, a senior fellow for defense budget studies at the non-partisan Center for Strategic and Budgetary Assessments think tank, said the FAA bill’s passage “shows that Congress is more than happy to ignore sequestration cuts until they start to present very visible impacts to people.”

“And (the Department of Defense) DoD should take a lesson from this,” Harrison said Monday, during a Defense Daily webinar on the Pentagon budget and sequestration. “While it is good policy and planning to try to mitigate the impacts of sequestration in the current fiscal year, if they are successful at doing that, it makes it virtually certain they’re going to stay at this lower level of funding in future years.”

Lawmakers who oppose sequestration have wrestled this issue, of with whether it is wise to let the negative impacts of the cuts play out to bolster public opposition.

Mackenzie Eaglen, a resident fellow at the conservative American Enterprise Institute think tank, said during the webinar that the FAA bill’s passage doesn’t change her skepticism about Congress and the White House agreeing to a deal to stop sequestration any time soon.

“There are tweaks and changes throughout this process to sequestration,” Eaglen said. “However, for DoD the books are largely closed on the outcome of sequestration in fiscal year ’13.”

She noted that the Pentagon is planning to send Congress requests to reprogram funding in its coffers as well as an “offset supplemental” legislative request for more funding. Both of those moves are intended to help the Pentagon grapple with $41 billion in near-term sequestration cuts in FY ’13, running from March 1 to Sept 30.

“However, none of these are going to undo or replace or repeal sequester for DoD,” Eaglen said

Larry Korb, a senior fellow at the left-leaning Center for American Progress think tank, argued during the webinar that the Pentagon should have laid out a plan for sequestration before it hit, “rather than pretending it would go away.”

The Pentagon’s FY ’14 budget proposal also does not factor in the sequestration cuts for that year, because Obama’s overall budget offers a plan that Republicans have rejected to stop sequestration.

“To keep pretending that it’s not going to happen makes it worse,” Korb said, pointing to reports that the military services may have different plans from each other for furloughing civilian employees because of sequestration.

Obama told reporters at the White House Tuesday that if he didn’t sign the FAA bill Republicans would blame him for the continued flight delays. Still, he stood by his call for Congress to agree on an alternate plan to the  sequester made up of spending cuts and tax increases.

“The only way to do that is for them to engage with me on coming up with a broader deal,” Obama said during a press conference. “Frankly, I don’t think that if I were to veto, for example, this FAA bill, that that somehow would lead to the broader fix. It just means that there’d be pain now, which they would try to blame on me, as opposed to pain five years from now. But either way, the problem’s not getting fixed. The only way the problem does get fixed is if both parties sit down and they say, how are we going to make sure that we’re reducing our deficit sensibly.”