The autopsy findings detected traces of narcotics with Jeffrey Reynolds and Mark Kennedy, both 44, CNN reported.
Further investigations will be conducted to determine whether Reynolds and Kennedy consumed anything that could have brought on the conditions, police said.
In a statement, police said a preliminary investigation report "includes suspicion of drug use, as indicated by the presence of a syringe and traces of heroin which were found in the cabin."
The men were employed by Trident Group, a maritime security services firm based in Virginia. Trident Group President Tom Rothrauff said Reynolds and Kennedy were former Navy SEALs.
The ship arrived in the Seychelles Feb. 16 with a 24-man crew and was scheduled to depart Feb. 18, the same day a colleague found the bodies, Seychelles police said.
"Based on our experience with the contractor, this is an isolated incident," Maersk said.
The shipping company said new drug tests would begin immediately and the company's shore-leave policy was under review.
The 500-foot Maersk Alabama was the target of an attempted hijacking off east Africa in 2009, which inspired the Oscar-nominated 2013 film "Captain Phillips" with Tom Hanks in the title role.