Reversing the president’s decision to delay the purchase of one Virginia-class submarine was the top priority this year for submarine advocates in Congress, U.S. Rep. Joe Courtney said Wednesday.

With both the Senate and House of Representatives agreeing to fund the submarine in the National Defense Authorization Act, Courtney, D-2nd District, said it’s “too early to do a victory dance in the end zone, but we’re in the red zone.”

The bill authorizes a 1.7 percent pay raise for military personnel and rejects the administration’s request for new rounds of base closures in 2013 and 2015. The Naval Submarine Base in Groton was nearly closed during the 2005 round.

The conference committee will begin working out the differences between the Senate and House versions of the bill next week. Both contain $778 million in advance procurement funding so the Navy can purchase two Virginia-class submarines in 2014, which effectively locks the funding into the final authorization act.

The Senate passed the $631 billion defense bill, 98-0, Tuesday night; the House approved it in May.

Sen. Joe Lieberman, D-Conn., cautioned that the “Senate’s work on defense is not completed with the passage of this bill.” Congress has until the end of the year to prevent $1.2 trillion in automatic spending cuts — known as sequestration — from taking effect Jan. 2.

Lieberman said the cuts “will do significant damage to our national security if they are implemented,” and he will work with his colleagues “to ensure we avert the fiscal cliff while sparing further cuts to America’s defense.”

Congress also gave the Navy the contracting authority for a five-year block, from 2014 to 2018, of up to 10 new submarines instead of capping the total at nine, and said the Navy could pay for the parts and services for the submarines over a set number of years instead of having to fund the ships fully upfront.

The coalition of legislators, primarily from Connecticut, Rhode Island and Virginia, lobbied for the incremental funding approach, which has been used with aircraft carriers but not with submarines.

But, Courtney said, the “2014 dip” was “the biggest step backward that we faced after years of progress.”

The president’s proposed budget had called for building one Virginia-class submarine in 2014 instead of two, and two subs in 2018 instead of one to save money now.

The work on the second submarine in 2014 translates to about 2 million man hours annually for five years at Electric Boat and Newport News Shipbuilding in Virginia — enough work to keep 800 to 1,000 people busy.

Bob Ross, executive director of the state’s Office of Military Affairs, said it would have been counterintuitive to make cuts to the program at a time when submarines are going to play a more prominent role in national security strategy.

The Virginia-class program should receive $4.9 billion, including $3.2 billion to build two submarines in 2013 and $1.7 billion to purchase parts with long lead times for two submarines in 2014 and 2015.

Sen. Richard Blumenthal, D-Conn., said the defense bill means “more jobs and economic growth for our state as it supports weapons and defense products made in Connecticut by Connecticut workers.”

On Wednesday, the House adopted the Senate’s version of the Coast Guard Authorization Act and made changes to the policy bill. The bill now returns to the Senate.

There was an attempt in November 2011 to amend the bill to change the admissions process at the Coast Guard Academy. The other military service academies admit students by congressional nomination, while the Coast Guard Academy traditionally has admitted students on the basis of academic merit.

The amendment failed, and the current bill does not include the proposal.

j.mcdermott@theday.com