KINGS BAY NAVAL SUBMARINE BASE, Ga. (AP) — The first U.S. women allowed to serve aboard submarines will be reporting for duty by 2012, the Navy said Thursday as the military ordered an end to one of its few remaining gender barriers.

The cramped quarters and scant privacy aboard submarines, combined with long tours of up to 90 days at sea, kept them off-limits to female sailors for 16 years after the Navy began allowing women to serve on all its surface ships in 1994.

There were some protests, particularly from wives of sub sailors, after the military began formulating a plan last fall. But it received no objections from Congress after Defense Secretary Robert Gates notified lawmakers in mid-February that the Navy intended to lift the ban. The deadline for Congress to intervene passed at midnight Wednesday.

Rear Adm. Barry Bruner, who led the Navy’s task force on integrating women onto submarines, brushed aside questions from reporters about the potential for sexual misconduct or unexpected pregnancies among a coed crew.

‘‘We’re going to look back on this four or five years from now, shrug our shoulders and say, ‘What was everybody worrying about?’’’ said Bruner, the top sub commander at Kings Bay Naval Submarine Base in coastal Georgia, where the announcement was made.

The first group of women will consist entirely of officers assigned to guided-missile attack submarines and ballistic-missile submarines, which have the most living space in the Navy’s fleet.

They’ll be assigned to two subs based at Kings Bay on the East Coast, and two others at the West Coast naval hub of Bangor, Wash.

Limiting women to officer slots lets the Navy, for a time at least, sidestep the more vexing and cost-prohibitive problem of modifying subs to have separate bunks and bathrooms for enlisted men and women. Enlisted sailors make up about 90 percent of a sub’s 160-sailor crew. No timeline was given for integrating enlisted women onto subs.

Bruner said 24 women will be able to begin training for submarine officers, which takes at least 15 months, this summer. They’ll be divided up so that three women are assigned to each sub’s two rotating crews.

That grouping will let all three women aboard a sub share a single stateroom for sleeping. The single bathroom shared by a sub’s 15 officers will be equipped with a sign to show if it’s occupied by men or women.

Otherwise, most changes will likely be behavioral shifts by male sailors who aren’t used to having women aboard, said Lt. Cmdr. Daniel Lombardo, executive officer of the submarine USS Alaska.

‘‘The guys are probably used to walking to the restroom in their boxer shorts and stuff,’’ Lombardo said. ‘‘But all in all, I think the adjustments for the crew are going to be minor.’’

One of the most difficult groups to win over on the concept of coed subs has been women themselves — at least those who are married to submarine sailors.

On blogs and online networking sites, wives of submariners have warned that close contact between the sexes at sea could lead to temptation and allegations of sexual harassment.

‘‘There’s a lot of Navy wives worried about their husbands cheating,’’ said Petty Officer 1st Class Glenn Gray, a missile technician on the Alaska, who said his wife isn’t crazy about the idea. ‘‘I’ve told her not to worry, because I’m married to her.’’

Bruner said that when his task force talked with the wives of submariners, the wives’ primary concern wasn’t that their husbands might cheat. Instead, most were concerned that unqualified women would be allowed onboard the subs to the detriment of the crew and potentially take jobs from their husbands.

Bruner said he found the opposite was true: If women are held to the same performance standards as men, as the Navy plans, allowing women aboard subs will ensure that each sub is staffed with the most capable staff possible.

The Navy declined several requests by The Associated Press to interview female sailors and cadets at U.S. bases about the policy change.

Women are currently allowed to serve on subs in a few countries, including Australia, Canada, Norway, Spain and Sweden.

About 52,446 women serve on active duty in the U.S. Navy, or about 15 percent of total personnel. Navy officials said women also make up about half the pool of potential recruits with educational degrees that qualify them for training as submarine officers.

‘‘We literally could not run the Navy without women today,’’ Navy Secretary Ray Mabus said in a statement.

Sailors interviewed aboard the Alaska at Kings Bay on Thursday said they’re not opposed to the change.

But Petty Officer 2nd Class Chris Merceri predicted there will be ‘‘a little more anxiety’’ when female officers come aboard for the first time.

‘‘Everybody’s going to be really up on their P’s and Q’s, very formal and careful of what they do,’’ Merceri said. ‘‘After that, everyone will be relaxed and comfortable. It’ll be another day at work.’’