House and Senate lawmakers are set to hammer out a final version of major annual defense policy legislation to send to President Obama — and the ability of military chaplains to officiate over same-sex weddings will be part of the discussion.

Late Thursday, the Senate approved by a 93-7 vote its version of the fiscal year 2012 defense authorization bill, which authorizes $662 billion in spending for military programs and troop compensation. The House passed its version of the bill in May, which authorizes $690 billion in defense funds.

The bills diverge in numerous ways and the conference committee will have to resolve the differences. But one issue in particular that is stirring up social conservatives and LGBT advocates is the involvement of military chaplains and facilities in same-sex weddings.

On Wednesday, the Senate approved by voice vote as part of its version of the bill an amendment by Sen. Roger Wicker (R-Miss.) allowing military chaplains to opt out of performing same-sex marriage ceremonies.

“A military chaplain, who, as a matter of conscience or moral principle, does not wish to perform a marriage may not be required to do so,” the amendment states.

The amendment is apparently in response to guidance the Pentagon issued on Sept. 30 permitting chaplains to officiate over same-sex weddings if they so choose. On the same day, the Defense Department issued guidance saying military bases could be used for same-sex weddings, although the Wicker amendment makes no mention of the use of military facilities.

Wicker’s measure is likely an attempt to appease social conservatives, who have been riled up over the guidance since it was made public. Just Wednesday, the Republican-controlled House Armed Services Personnel Subcommittee held a closed briefing with Pentagon general counsel Jeh Johnson and Navy counsel Paul Oostburg Sanz on the legal rationale that led to the Pentagon guidance.

But the Wicker amendment won’t produce any change because it reiterates the administration’s policy of giving chaplains the option of whether or not to take part in same-sex weddings.

Aubrey Sarvis, executive director of the Servicemembers Legal Defense Network, said the passage of the amendment into law wouldn’t change anything.

“This amendment does nothing new as it relates to the rights of chaplains,” Sarvis said. “Indeed, the new Senate language is a restatement of the protections and guarantees that have always been there.”

In a statement, Wicker said the amendment would be a way to “protect” chaplains from being involved in same-sex weddings.

“This amendment will allow the chaplains of our armed forces to maintain the freedom of conscience necessary to serve both their nation and their religion without conflict,” Wicker said.  “Protections for military chaplains should be guaranteed in any policy changes being implemented.”

But the amendment stands in contrast to a measure in the bill passed by the House, which would have an impact on a chaplain’s ability to conduct weddings.

Language that was inserted by House Armed Services Committee Chair W. Todd Akin (R-Mo.) during committee markup outright prohibits military chaplains or civilian Pentagon employees from assisting with or officiating at a marriage ceremony.  The same provision also prohibits the use of military bases for these purposes.

Conferees will have to decide whether to address the issue by agreeing on either the House or Senate language, or by including no language at all related to military chaplains and facilities in the final bill.

Michael Cole-Schwartz, a spokesperson for the Human Rights Campaign, said his organization wants conferees to omit any language related to military chaplains.

“We want to see the [defense authorization bill] signed into law without any language that would harm LGBT service members or restrict the religious liberties of chaplains,” Cole-Schwartz said. “We’ll be working with our allies on the conference committee toward that outcome.”

But social conservatives seem bent on pushing for the more restrictive provision in the House version of the legislation.

Steve Taylor, an Akin spokesperson, said his boss will push for his language in the report that will be produced by conferees.

“The two amendments are similar but not equivalent so it is fair to say the congressman still wants to see his amendment prevail,” Akin said.

House Armed Services Committee Chair Buck McKeon (R-Calif.) has previously said he’d rather see no defense authorization bill pass than one that didn’t include language prohibiting military chaplains from participating in same-sex weddings.

Asked whether the Senate language would be sufficient, McKeon spokesperson Claude Chafin said he’s “bound by a policy not to discuss conference items ahead of the conference.”

The timing isn’t yet known for when the conferees will complete their work on the defense authorization bill, but the issue related to same-sex weddings is just one issue among others that conferees will have to resolve. And it’s possible Congress could send a defense authorization bill to the president that he’ll ultimately veto.

The White House issued a veto threat over the Senate version of the bill over the inclusion of an amendment that would require military custody of terrorist suspects and allow indefinite detention of some without trial.

In the House bill, the Obama administration objects to provisions that would require military trials for suspected terrorists, limit the president’s authority to transfer terrorist suspects from the naval facility at Guantanamo Bay, Cuba, to U.S. installations, and make it difficult for the administration to move detainees to foreign countries.

And military chaplains conducting same-sex weddings isn’t the only LGBT-related issue. The Senate bill contains language that would repeal Article 125 of the Uniform Code of Military Justice, the long-standing military law classifying consensual sodomy for both gay and straight service members as a crime.

The Pentagon called for repeal of the sodomy ban in the report issued last year on “Don’t Ask, Don’t Tell.” The Senate bill has the repeal language, but it’s not found in the House legislation, so conferees will have to hammer out the difference.

The House bill also contains language reaffirming that the Defense Department abides by DOMA in regulations and policies. However, the provision, inserted by Rep. Vicky Hartzler (R-Mo.), wouldn’t affect anything because the Pentagon as an arm of the federal government already has to comply with DOMA.

Additionally, the House bill has language that would expand the requirement for “Don’t Ask, Don’t Tell” repeal certification beyond the president, the defense secretary and the chair of the Joint Chiefs of Staff to include input from the four military service chiefs. But the issue is moot because “Don’t Ask, Don’t Tell” repeal certification has already happened and the military’s gay ban was lifted on Sept. 20.