Traces of narcotics and hypodermic needles found with the bodies of the men suggested the deaths resulted from drug overdose, a Seychelles government official told CNN on Thursday.
Maersk released a statement saying that this was an isolated incident based on their experience with the contractor and they've initiated a review.
They are now working with the Trident Group to ensure that security employees adhere to their zero tolerance policy regarding the use of drugs and alcohol.
The vessel was moored at Port Victoria in the Indian Ocean archipelago. The men, who are Americans, both 44, were found dead on Tuesday. CNN first learned about this on Twitter.
Police in the Seychelles said the two men were part of a 24-member crew that arrived on Sunday and were expected to leave Tuesday.
The men were former Navy SEALS, according to Tom Rothrauff, the CEO of The Trident Group, the company they were employed by.
One of the men has been identified as Mark Kennedy. Kennedy's resume shows he worked 16 Years in U.S. Navy, including 13 as SEAL. He was discharged in 2010 and began working for the Trident Group in Virginia Beach.
"A postmortem will be carried out this week in order to establish the cause of their sudden deaths," police said, adding that the police investigation is ongoing.
The Maersk Alabama was targeted by Somali pirates in an attempted hijacking off the east coast of Africa in 2009. The 2013 film "Captain Phillips" is based on the incident.
Kevin N. Speers, a senior director for Maersk Line Limited, said in a statement that the security contractors boarded the vessel on January 29, and that their deaths were were "not related to vessel operations or their duties as security personnel."
Maersk Line Limited contracts with Trident Group in accordance with U.S. Coast Guard security directives, Speer said in the statement.
"Contracted security is part of anti-piracy protection plans to safeguard crews and vessels," Speer said. "In Maersk Alabama's case, she is persistently in high-risk areas since she provides feeder service to the east coast of Africa. The vessel was cleared to complete cargo operations, and she is now at anchor awaiting further instructions."
Senior Chief Petty Officer Daniel Tremper said the U.S. Coast Guard had been notified about the deaths of two U.S. citizens and is investigating, but "due to the nature of the investigation, that will be about all that we can provide right now."
State Department spokeswoman Marie Harf confirmed the men were U.S. citizens. The Coast Guard is involved in the investigation because the Maersk Alabama is a U.S.-flagged ship, Harf said.
The bodies were found by a colleague who went to check in on one of the men in a cabin at about 4:30 p.m. Tuesday, Seychelles police said.
In April 2009, four armed pirates attempted to hijack the Maersk Alabama 380 miles off the coast of Somalia. After the crew sank the pirates' vessel and foiled their efforts to take control of the container ship, the pirates took the ship's captain, Richard Phillips, hostage on a lifeboat. The incident ended four days later when Navy sharpshooters killed three of the pirates and captured the fourth. Phillips was unharmed.
The ship was attacked by pirates again in November 2009, but armed security personnel fought them off.
CNN's Michael Martinez and Deanna Hackney contributed to this report.