Defense Secretary Robert Gates gave cover to President Barack Obama on Thursday to sign off on a massive omnibus spending bill stuffed with thousands of earmarks totaling more than $8 billion.

It would be “the worst of all possible worlds” if Congress passed a yearlong continuing resolution in place of the $1.2 trillion omnibus bill being debated on Capitol Hill, Gates told reporters during a briefing.

“I don’t much like earmarks,” he said, referring to the omnibus pending before the Senate. But passing a long-term CR as an alternative “would be a gigantic problem” for the Defense Department because it would mean budget shortfalls and little flexibility with programming.

Republicans have been railing against the size of the spending package unveiled this week by Senate appropriators, despite many of those same GOP lawmakers — including Senate Minority Leader Mitch McConnell (Ky.) — having previously requested millions of dollars of earmarks that made it into the package.

Speaker-designate John Boehner said Obama should reject the package in keeping with a pledge he made last month to work toward ending earmark spending.

“It is time for him to back up those words with action by making it clear that he will veto the omnibus spending bill written by Senate Democrats, which includes over 6,000 earmarks,” the Ohio Republican said.

White House Press Secretary Robert Gibbs said Thursday that Obama’s “strong preference” would be that the omnibus didn’t have any earmarks. But he signaled Obama would sign it because of the concerns voiced by Gates and Secretary of State Hillary Rodham Clinton about budget shortfalls affecting crucial operations in Afghanistan.

“We understand it is not perfect, but it is what the leaders in very important departments like the Pentagon and the State Department have said are necessary and needed,” Gibbs said at a briefing.