The email, obtained under a freedom of information request by conservative legal group Judicial Watch, shows that Admiral William McRaven, who heads the US Special Operations Command, told military officers on May 13 2011 that photos of bin Laden's remains should have been sent to the CIA or already destroyed.
The terror leader was killed by a US special operations team in Pakistan on May 2 that year.
Adm McRaven's order to purge the bin Laden material came 10 days after The Associated Press news agency asked for the photos and other documents under the US Freedom of Information Act.
Typically, when a freedom of information request is filed to a government agency under the Federal Records Act, the agency is obliged to preserve the material sought - even if it later denies the request.
On May 3 2011, AP asked Special Operations Command's Freedom of Information/Privacy Act Division office for "copies of all emails sent from and to the US government account or accounts" of then Vice Admiral McRaven referencing bin Laden.
A May 4 2011 response from the command's FOIA office to AP acknowledged the bin Laden document request and said it had been assigned for processing. The news agency did not receive a copy of the McRaven email obtained by Judicial Watch.
The Department of Defence FOIA office told AP in a February 29 2012 letter that it could find no McRaven emails "responsive to your request" for communications about the bin Laden material.
The Special Operations Command is required to obey rules established by the chairman of the Joint Chiefs of Staff that dictate how long records must be retained. Its July 2012 manual says records about military operations and planning are to be considered permanent and after 25 years, following a declassification review, transferred to the National Archives.
Last July a draft report by the Pentagon's inspector general first disclosed Adm McRaven's secret order, but the reference was not contained in the inspector general's final report. The email that surfaced yesterday was the first evidence showing the actual order.
In a heavily blacked-out email addressed to "gentlemen", Adm McRaven told his unnamed subordinates: "One particular item that I want to emphasise is photos; particularly UBLs remains. At this point - all photos should have been turned over to the CIA; if you still have them destroy them immediately or get them" a blacked-out location. UBL refers to bin Laden.
At the time the inspector general's report came out, a spokesman for the Special Operations Command referred questions back to the inspector general.
A CIA spokesman said at the time that "documents related to the raid were handled in a manner consistent with the fact that the operation was conducted under the direction of the CIA director", then Leon Panetta. The CIA statement also said "records of a CIA operation such as the raid, which were created during the conduct of the operation by persons acting under the authority of the CIA director, are CIA records".
In a Jan. 31 2014 letter to Judicial Watch in response to its request for all records relating to Adm McRaven's "directive to purge", the Pentagon's office of general counsel said it had been able to locate only document - his redacted email.
Judicial Watch president Tom Fitton said the email "is a smoking gun, revealing both contempt for the rule of law and the American people's right to know".