March 14, 2007  -- The Navy mobilized a search-and-rescue operation Tuesday night after it believed one of its submarines, the USS San Juan, had gone missing off the coast of Florida with 140 crew members aboard.

Communications were re-established early this morning, and it all appears to have been a case of miscommunication.

The concern was so high that Defense Secretary Robert Gates was notified of the situation overnight, as was White House national security adviser Stephen Hadley, who was preparing to brief President Bush with the news when communications were re-established with the missing submarine.

The Navy had also begun notifying the families of the 140 crew members that the submarine was missing. The incident is under investigation with the focus being on why the ship missed a pre-established communications period with surface ships.

Communications with the submarine were first lost at 7 p.m. Tuesday and were finally re-established by 5 a.m. today. The ship reported no problems, and both crew and officers were unaware of the effort under way to locate them.

According to Lt. Cmdr. Chris Loundermon, a spokesman for the Navy's Submarine Force, "They were operating as … though normal … and had missed a communication period they were not aware of."

According to Loundermon, no mechanical problems were found aboard the submarine and officials were looking at why the submarine had missed its communication period.

The Los Angeles class submarine, based in Groton, Conn., was operating off the coast of Jacksonville, Fla., as part of predeployment training with the USS Enterprise Carrier Strike Group when communications were lost.

Navy officials say the search was launched after surface ships spotted what appeared to be a red flare in the vicinity of where the submarine had been operating. A red flare is an indicator that a ship is in distress. With the loss of communications, a search-and-rescue effort was immediately launched.

During exercises, surface ships have a general idea of where submarines are operating underwater, but still have a hard time locating them. A Navy official said to ABC News, "It's like any other adversary. We hope they can't find them. They're doing their mission of being seen, but unseen."

The Navy also notified the International Submarine Escape and Rescue Liaison Office, based in Norfolk, Va. ISMERLO contacts international partners to deploy rescue systems in the event of a submarine accident. The fatal sinking of the Russian submarine Kursk in August 2000 prompted an international rescue effort; 118 crew men died in that incident.

Family members were called at 4 a.m. today with word that communications had been lost with the submarine. Two hours later they received the good news that communications had been re-established.

A family meeting was held today for 30 family members to explain what happened and to reassure them that the USS San Juan was operating as normal.