The White House threatened yesterday to veto the Pentagon policy bill before the Senate, citing multiple qualms with it including proposals to stop the retirement of aircraft and block funding for an international missile-defense program.

Meanwhile, the Senate took steps yesterday, during its second day debating the lengthy fiscal year 2013 defense authorization bill, that put it at odds with the House on the hot-button topics of a potential East Coast missile-defense site and Pentagon alternative-energy development.

Thus, while the Senate neared final passage of the policy-setting legislation last night, the measure still has multiple hurdles to overcome before becoming law, if it does. The White House similarly threatened to veto the defense authorization bill the House passed in May. After senators pass the bill before them, perhaps today, Senate and House negotiators will have to agree on a final version to place before President Barack Obama.

The Office of Management and Budget (OMB) said yesterday the Obama administration has “serious concerns with provisions” in the Senate bill that clash with the Pentagon’s FY ’13 budget request, limit the executive branch’s authorities, and “constrain the ability of the armed forces to carry out their missions consistent with the new defense strategy.” It says Obama’s advisers would recommend he veto the bill in its current form, pointing to eight sections to which it “strongly objects.”

Those sections include one that would block the Air Force’s plan to retire or divest more than 200 Air National Guard and Air Force Reserve aircraft over the next five years–something the House-passed bill also rejects.

“These provisions would force (the Department of Defense) DoD to operate, sustain, and maintain aircraft that are in excess to national security requirements, as defined by the new defense strategy, and are not affordable in an austere budget environment,” the OMB says in a Statement of Administration Policy on the Senate bill.

The administration also sticks up for the Medium Extended Air Defense System (MEADS), a U.S.-German-Italian missile-defense program the United States previously tried to exit. The Senate bill, like the House-passed one, prohibits the Pentagon from spending the $400.9 million it requested for MEADS. The SAP warns not funding the program in FY ’13 could harm the United States’ relationship with Germany and Italy “on a much broader basis, including future multinational cooperative projects.”

The OMB also “strongly objects” to authorization in the Senate bill for an incremental funding setup–which is different than advanced-procurement funding–for the Virginia-class submarine and Space-Based Infrared System satellites.

The SAP also cites parts of the Senate bill to which it simply “objects”–but not “strongly”–including unrequested authorizations in it for the advance procurement of more F/A-18E/F Navy fighters and upgrades to M-1 Abrams tank, the latter of which Congress wants to fund to prevent a temporary shutdown of the production line.

The Senate, meanwhile, dug into the authorization bill on the floor yesterday, working into the night to pare down a list of roughly 300 proposed amendments.

Senate Armed Services Committee (SASC) member Kelly Ayotte (R-N.H.) withdrew an amendment to require a report from the Pentagon by the end of 2013 on three possible East Coast locations to bury missile interceptors. Sens. Susan Collins (R-Maine) and Joe Lieberman (I/D-Conn.) had co-sponsored it. Yet SASC Chairman Carl Levin (D-Mich.) has repeatedly said military leaders tell him there is no need for such an East Coast missile-defense site.

Ayotte, for her part, argued “that many analysts believe that Iran will be able to develop the capacity to strike the mainland of the United States with an intercontinental ballistic missile by 2015,” and the U.S. should use existing technology to protect the eastern seaboard.

Still, the House-passed bill includes language regarding such a location, she noted, which could still make it into the final House-Senate legislation.

The House measure authorizes $100 million for planning an East Coast site after the Missile Defense Agency crafts a proposal for it, and also requires the Pentagon to produce an environmental-impact statement on possible locations.

As expected, the Senate passed an amendment yesterday, by a 54-41 vote, to remove language SASC Republicans previously added to the bill that would ban the military from building a biofuels refinery unless specifically authorized by law.

The successful pro-biofuels amendment, from Sen. Kay Hagan (D-N.C.), is similar to one from Sen. Mark Udall (D-Colo.) that the Senate passed by a 62-37 margin Wednesday. Udall’s successful measure removed language from the bill that would prohibit the Pentagon from buying alternative fuels if they cost more than traditional fossil fuels.

The House’s defense authorization bill would place limits on the Pentagon’s alternative-energy endeavors. How to resolve the biofuels matter will be a major issue for the heads of the Senate and House armed services committees to resolve, congressional aides said.

Most of the amendments the Senate passed yesterday were non-controversial measures agreed to by voice vote. Those include a measure from Sen. John Hoeven (R-S.D.) to add a “sense of Senate” to the bill saying the United States is committed to retaining and modernizing a nuclear triad of land-based intercontinental ballistic missiles, submarine-launched ballistic missiles, and nuclear-capable heavy bombers.

Another successful amendment, from Sen. John Barrasso (R-Wyo.), says the defense secretary may “retain intercontinental ballistic missile launch facilities currently supporting deployed strategic nuclear delivery vehicles within the limit (under international agreements) of 800 deployed and non-deployed strategic launchers.”