Debate over the fiscal 2009 war supplemental now moves to the Senate floor after the House on Thursday passed its bill and Senate Appropriations approved its version.

Much of the House debate focused on the fate of the Guantanamo Bay detention facility and its prisoners, with Republicans arguing that the bill didn’t do enough to prevent detainees from possibly being released in the United States. Democrats had engineered a bill modification that barred the use of funds to release detainees on American soil and prevented their transfer here until after President Obama submitted a comprehensive plan, but Republicans said it wasn’t sufficient.

Many liberal anti-war House Democrats expressed their opposition to the bill, arguing that it allows for an open-ended expansion of U.S. military activities in Afghanistan.

The $96.7 billion bill passed overwhelmingly, 368-60, with only 51 Democrats voting against it. Republicans also overwhelmingly supported the measure, voting 168-9. More partisan votes occurred earlier as a GOP motion to recommit the bill fell, 191-237, largely along party lines (among other things, the motion sought to bolster anti-drug funding along the U.S.-Mexico border), as did a GOP effort to defeat a procedural motion and allow the consideration of amendments. The floor rule adopted for the bill prohibited all amendments.

Senate Appropriations approved its $91.3 billion measure, 30-0, after adopting a handful of non-controversial amendments. The Senate bill’s funding total is $1.3 billion more than requested, including the midweek administration request for $5 billion to support an increased U.S. contribution to the International Monetary Fund. But it is about $5.4 billion below the House bill’s total (which does not include the IMF provisions). The Senate measure would fully fund the $73.7 billion Obama requested for the Pentagon, but would shift $700 million within that total to other accounts, such as military construction, homeland security, or State Department accounts. Like the House bill, it provides for the acquisition of four F-22 fighters, but does not include funding to shut down that aircraft production line. It also follows the House lead in providing more funds above the president’s request for additional Mine Resistant Ambush Protected troop transport vehicles and for a similar protected vehicle that would be better suited to the terrain and poor roads in Afghanistan. Unlike the House bill, it includes no unrequested funding for C-17 and C-130 cargo aircraft. However, Inouye assured supporters of the C-17 aircraft that he would work to continue the program, which Obama proposes to terminate.

The Senate bill includes $1.5 billion as requested by the White House for pandemic flu response activities, and, like the House bill, directly distributes it to agencies rather than giving it to OMB to parcel out, which was the administration’s preference. Of that total, $900 million would go to Health and Human Services, $190 million to Homeland Security, $110 million to Veterans’ Affairs, $100 million to USDA, $50 million to FDA and $150 million to USAID to help with the international response. The House bill provides a total of $2 billion, with $1.85 billion of that going to HHS and $200 million for international activities through a White House fund. Senate Labor-HHS-Education Appropriations Chairman Tom Harkin, D-Iowa, noted that questions regarding total funding levels and distribution between agencies would have to be sorted out in conference.

Senate floor consideration on the measure will begin no earlier than Tuesday, leaving little time for the two chambers to reconcile their versions before leaving for the Memorial Day recess at the end of the week.