The officer overseeing the US naval base at Guantanamo Bay has been sacked after he had an alleged affair with a woman whose husband was recently found dead at the base, officials said Thursday.

Captain John Nettleton was relieved of duty on Wednesday "due to loss of confidence in Nettleton's ability to command," the US Navy said in a statement.

The officer was under investigation in connection with the death of Christopher Tur, a civilian who was found dead in the waters off the American base in southeast Cuba, a US official, who spoke on condition of anonymity, told AFP.

Tur's body was discovered by the US Coast Guard after he had been reported missing by his wife, who is also a civilian, said the official, confirming media reports.

Naval criminal investigators learned of Nettleton's alleged affair as they probed the circumstances of Tur's death, the US official said.

Nettleton has been temporarily reassigned to a staff job in Jacksonville, Florida while Captain Scott Gray, the chief of staff to the commander of the navy's southeast region, has been assigned as acting commanding officer at Guantanamo.

Nettleton had begun his job at Guantanamo Bay in June 2012.

The naval base hosts the controversial military prison that houses terror suspects and also provides logistical support for naval ships operating in the Caribbean region.