The Maersk Alabama was the ship commandeered by Somali pirates in 2009, a pirating incident that inspired the 2013 movie "Captain Phillips."
Seychelles police said a colleague found the men's bodies Tuesday. Police said autopsies would be performed this week to determine the cause of the two 44-year-old men's "sudden deaths," CNN reported.
Police said the Maersk Alabama arrived in the Seychelles Sunday.
Tom Rothrauff, president of the Trident Group, the Virginia company that employed the two men, said they were former SEALs.
"It's bizarre. Of course, it's a shock. They're all great guys," Rothrauff said. "I'm absolutely clueless as to what happened."
Maersk Line Ltd. senior director Kevin N. Speers indicated in a statement Trident provides anti-piracy security for the shipping company, which operates in regions at high risk for attacks by pirates, but that the deaths of the two men, who boarded the vessel Jan. 29, were "not related to vessel operations or their duties as security personnel."
Senior Chief Petty Officer Daniel Tremper said the U.S. Coast Guard was investigating the deaths, but "due to the nature of the investigation, that will be about all that we can provide right now."