Republicans on the Senate Appropriations Committee agreed Wednesday to adopt many aspects of a House-backed restructuring of the panel, but the changes will not prevent the two chambers from clashing when it comes time to reconcile several disparate spending bills later in the year.

The Senate rejected the House’s plan to eliminate three subcommittees, electing to dismantle only the subcommittee on Veterans’ Affairs, Housing and Urban Development and independent agencies. The resolution leaves the Senate with 12 subcommittees and the House with 10.

“We’re resigned to the reality that this is best we can do and want to do,” said Sen. Larry Craig (R-Idaho), a member of the committee.

Senate Appropriations Chairman Thad Cochran (R-Miss.) said the unanimous vote Wednesday afternoon among panel Republicans marked the end of discussions between the House and Senate on the topic.

“I think the organization is coherent enough so that no further changes need to be made by the House,” Cochran said.

Cochran said he would discuss the Senate’s decision with House Appropriations Chairman Jerry Lewis (R-Calif.) and expressed optimism about avoiding a year-end catchall spending bill, known as an omnibus.

But given the structural differences that remain between the House and Senate subcommittees, an omnibus or smaller packages of bills, dubbed minibuses, may be necessary.

Senators also noted that they are still angry with the House for trying to force the Senate’s hand on reorganization. Two weeks ago, the House adopted its plan after just a week of negotiation with Senate, without waiting for the chamber’s consent.

“Are there still reservations in the committee about the way the House did this? Absolutely,” Craig said.

Still, the Senate largely mimicked the way in which the House spread VA-HUD’s varied jurisdiction over nine other subcommittees.

But in a dramatic departure from the House approach, the Senate stripped the Commerce-Justice-State subcommittee of its jurisdiction over the State Department and the judiciary and replaced it with jurisdiction over NASA and the National Science Foundation, among other programs. The new panel would be called the Commerce, Justice and Science subcommittee.

Funding for the State Department would be transferred to the foreign operations subcommittee, which is currently headed by Senate Majority Whip Mitch McConnell (R-Ky.). The House’s current subcommittee structure keeps the State Department under the CJS subcommittee, and the differences between the two chambers, if left unresolved, could create a situation where the CJS and foreign operations bills have to be merged in conference committee.

In another wrinkle for future House-Senate negotiations, the Senate did not split off about $36 billion in Defense Department accounts from the Defense subcommittee, as the House did. The House would put some personnel accounts in a new military quality of life and Veterans’ Affairs panel.

The Senate also declined to eliminate the legislative branch and District of Columbia subcommittees, though that decision does not appear to cause as much trouble for future conference committees. The full House panel is charged with overseeing legislative branch affairs, while the new House Transportation subcommittee will absorb funding for the nation’s capital.

Meanwhile, both chambers would give funding for federal courts to the Transportation panel.

The Senate did decide to give the military construction panel jurisdiction over the Veterans’ Affairs Department, despite the objections of Craig, who also serves as Senate Veterans’ Affairs chairman. Craig had initially considered using his seniority on the Appropriations Committee to seize the panel from Sen. Kay Bailey Hutchison (R-Texas) if veterans were forced to compete for funds with the military as part of the same committee.

But Hutchison said Craig was “magnanimous” and agreed to let her keep the gavel.

Current Transportation subcommittee Chairman Richard Shelby (R-Ala.) will take the reins of the revamped Commerce panel from Sen. Judd Gregg (R-N.H.).

“I’ve been looking at it with interest for a number of years,” Shelby said of taking over a new CJS panel.

Shelby was forced to look for another spot when Sen. Kit Bond (R-Mo.), who lost the VA-HUD chairmanship in the restructuring, opted to take over the renamed Transportation, Treasury, the judiciary and Housing and Urban Development subcommittee. The panel is considered a good fit for Bond, who as chairman of the transportation and infrastructure subcommittee on the Senate Environment and Public Works Committee, is also in charge of this year’s rewriting of the massive highway funding bill.

Gregg will take over the Homeland Security subcommittee chairmanship from Cochran, who offered to give up Homeland Security to ensure that displaced chairmen like Gregg would still have plum subcommittee slots.

Still, Gregg was not pleased about having to give up CJS.

“The chairman was very generous in offering to give up Homeland Security, but I still like the CJS committee,” Gregg said.

Sen. Mike DeWine (R-Ohio) will retain his gavel on the District of Columbia subcommittee, and Sen. Sam Brownback (R-Kan.), who did not have a subcommittee chairmanship until now, will take over the legislative branch subcommittee.

Other subcommittee chairmen remain unchanged, but many of their panels have gained jurisdiction. For example, Sen. Conrad Burns (R-Mont.), who will chair a renamed Interior and related agencies subcommittee, will now oversee the Environmental Protection Agency, among other things. However, Interior will lose several energy-related accounts to Sen. Pete Domenici’s (R-N.M.) Energy and water subcommittee. Both moves mirror the House structure.

A few GOP Senators, perhaps engaging in a bit of wishful thinking, suggested the House should now adopt the Senate’s reorganization plan.

“The House ought to come forward now and settle this problem and give us the same type of committees,” said Sen. Ted Stevens, the former chairman of the full Appropriations Committee and current chairman of the Defense subcommittee.

House Appropriations spokesman John Scofield said Lewis would continue to keep up a dialogue with the Senate, but would not negotiate in the press.

“I think we’ll continue our posture of talking with our friends in the Senate,” Scofield said.

Lewis has said in the past that he might be willing to further tinker with his panel’s organizational structure to make the two chambers’ spending panels more compatible.

One knowledgeable House GOP aide said it was unlikely that the House would restore the Defense accounts to the Defense subcommittee, but held out the possibility that the House may decide to give jurisdiction over the State Department to the foreign operations subcommittee.