( CNN ) The commanding officer of the U.S . Naval Station in Guantanamo Bay , Cuba , has been relieved of duty `` due to loss of confidence '' in his `` ability to command , '' the Navy says . At issue is an allegation of an inappropriate relationship , a U.S. military official told CNN . Capt . John R. Nettleton has been temporarily reassigned to a post in Jacksonville , Florida , the Navy said in a statement released Wednesday . The Navy did not say why , withholding further details `` due to an ongoing NCIS ( Naval Criminal Investigative Service ) investigation . '' But a U.S. military official said that in the course of investigating the death of a civilian , the Navy received information alleging that Nettleton was engaged in an inappropriate relationship with the civilian 's wife . According to the Miami Herald , Christopher Tur was found dead in the waters off Guantanamo Bay on January 11 . He had been a worker at the base commissary . Having an affair violates military law -- the Uniform Code of Military Justice -- and could in itself constitute grounds for Nettleton 's reassignment . There are initial indications that Tur 's death was a suicide , but no cause of death has yet been determined , according to one official with knowledge of the situation . Defense Secretary Chuck Hagel was asked about the story by reporters at the Pentagon on Thursday . He confirmed that Nettleton was no longer in command , but had no further comment . `` Well , the base commander has been relieved , '' said Hagel . `` It is now in the purview of appropriate authorities . So , I wo n't have anything to say specifically about that , which would be inappropriate . But the commander has been relieved and that is right . '' The Naval commander at Guantanamo Bay does not oversee the detention facility that President Barack Obama has vowed to close . Nettleton has been in charge since June 2012 . The decision to relieve him of his duties was made by Rear Adm. Mary M. Jackson , commander of Navy Region Southeast , the military said in a statement .
Capt . John R. Nettleton has been reassigned to Florida . An inappropriate relationship is alleged , according to a U.S. military official .