A lawmaker backing plans to restore a nuclear submarine to the Navy’s budget said current legislation on Capitol Hill would allow the service to add the vessel through a somewhat-unorthodox funding setup.

While the fate of many weapon systems is unknown amid ongoing budget deliberations in Washington, Rep. Joe Courtney (D-Conn.) said the Virginia-class submarine program is poised to receive at least one piece of good news from Congress: permission for incremental funding.

“Language that would have prohibited incremental funding” in the still-pending fiscal year 2013 defense appropriations bill was “eliminated,” Courtney said yesterday in the sidelines of the Surface Navy Association’s National Symposium in Arlington, Va.

The Navy previously planned to buy two Virginia submarines in FY ’14, which starts in October, but reluctantly cut funding for one of them last year in its official FY ’13 budget request to Congress because of fiscal constraints.

Defense authorizers like Courtney then rallied last year behind a plan–touted by Navy acquisition czar Sean Stackley–to add the second submarine back to the longterm budget through an incremental-funding setup. Such an arrangement, which is different from multiyear procurement, allows the service to spread costs over multiple years.

Yet defense appropriators initially balked at the incremental funding arrangement. House Appropriations Defense subcommittee Chairman C.W. “Bill” Young (R-Fla.) said he didn’t want to get into that trap of running a credit-card economy for the Defense Department.” (Defense Daily, May 14, 2012)

Defense authorizers’ support remained and the FY ‘13 defense authorization act, which Congress passed last month and President Barack Obama signed into law on Jan. 2, grants the Navy that rarely-used authority to fund the second FY ’14 vessel through incremental funding. The act also authorizes the Navy to buy 10 of the subs through a multi-year procurement–a move that supports its plan to buy two of the vessels each year in the coming years.

Still, there has been concern that the FY ’13 defense appropriations bill–which Congress still has not passed–would not allow the incremental funding. The Pentagon appropriations legislation the House passed last May denied such a funding setup, while the version the Senate Appropriation Committee passed in August supported it.

House and Senate appropriations negotiated a final FY ’13 defense bill last fall–behind closed doors–and that still-unseen compromise would allow incremental funding for the FY ’14 Virginia submarine, according to Courtney. He said the legislation is “silent on” the matter and does not outright ban such funding.

He said if Congress passes a final FY ’13 appropriations bill as he said it is now written–“silent” on the incremental funding–then “the Navy has its guidance.”

Congressional aides were not available to confirm the FY ’13 appropriations measure would not ban incremental funding yesterday, when the House and Senate were not in session.

Courtney, though, is among the lawmakers who most-closely track the Navy’s plans to each year buy two of the Virginia submarines. The vessels are made by in his district by General Dynamics’ [GD] Electric Boat shipyard, as well as by Huntington Ingalls Industries’ [HII] Newport News Shipbuilding in Virginia.

Courtney was so associated in recent years with his advocacy of accelerating the service’s plan to double production of the vessels to two per year that he was nicknamed “Two Sub Joe.”

Courtney said yesterday he doesn’t understand HAC-D opposition to allowing the special incremental setup for the sub effort, which he maintained “has really proven its bona fides.”

The House Appropriations Committee’s report on the House-passed FY ’13 bill argued the Navy’s “own financial management regulations and policies prohibit incremental funding of large end items such as ships, except under certain circumstances, none of which apply in this case” of the Virginia sub.

“The Committee strongly supports these regulations and policies because fully funded end items do not commit future Congresses to obligations they may or may not agree with and also because they provide the ability to conduct much more complete, transparent, and rigorous program oversight,” states the report attached to the bill passed last May.

Courtney said he is confident the compromise House-Senate defense appropriations bill would not block the incremental funding.

He noted that the Navy is allowed to use incremental funding for aircraft carriers, so it is “not some radical concept.”

While people have opposed incremental funding for weapons programs that have risk, Courtney argued the Virginia effort is “a program that’s so mature at this point and it’s really proven its ability to (get) the budget right.”

Beyond the incremental-funding matter, Courtney said the “bigger problem” facing the Virginia submarine program is garnering funding in an actual FY ’13 defense appropriations bill.

The Pentagon, like the rest of the government, is running on a bare-bones continuing resolution (CR) in FY ’13 until March 27 that provides funding for programs near FY ’12 levels.

“If we just do CR funding for the rest of the year (for the submarine effort) then I think that everything  kind of falls apart,” he said.

Congress and Obama have to decide how deal with that FY ’13 budget as they battle over multiple fiscal matters. Those include whether to raise the nation’s debt ceiling and stop pending “sequestration” budget cuts, which are set to start tapping $500 billion from longterm defense spending starting in March.