Navy officials tell NBC News that Phillips reportedly took the cash from the ship's safe and handed it over to the pirates who then took the money along with Captain Phillips aboard one of the ship's lifeboats in an effort to escape.

But after one of the pirates was taken into custody and Navy SEALs shot and killed the three other pirates holding Phillips hostage aboard the lifeboat, the money was apparently nowhere to be found.

Navy investigators are questioning the Navy SEALs, who were the first ones on board the lifeboat immediately after the three pirates were killed, as well as the crew members from two U.S. warships and the Maersk Alabama.

Navy officials say the SEALs would have thoroughly searched the lifeboat for any weapons, explosives or evidence immediately after the rescue, but at this point it's not clear they discovered the money, or if they turned it over as evidence once they were back on board the U.S. warships.

According to one official, "We're talking to anyone who would have been anywhere near that money," or have any information about where it may have been prior to the rescue. "The investigation is in the very early stages."

The allegations arose during the FBI's investigation into Abdiwali Abdiqadir Muse, the only surviving pirate who's been indicted in federal court in New York on 10 charges, including piracy, conspiracy and hostage-taking.